Well, here is what I have on the separation of indvidual world governments and the Imperium:
LIMITED MEMBER WORLD AUTONOMY (LMWA)
Each world admitted into the Imperium under a Member World Charter (and not conquered), is allowed Limited Member World Autonomy, or LMWA. The LMWA allows a world's government and inhabitants specific freedoms in exchange for agreeing to certain duties.
LMWA, Freedoms
1-The internal politics, laws, and elections of a world will not be interfered with by the Imperial Government as long as the specified Duties and Restrictions are followed.
2-The Imperium will extradite criminals wanted on a Member World to that Jurisdiction if the Imperial Citizen is not already wanted by the Imperium or another Member World. In cases where the Imperial Citizen has committed a crime against the Imperium, Imperial Jurisdiction takes absolute precedence. In cases where more than one Member World has filed criminal charges against an Imperial Citizen, the local Ruling Noble will rule on who is allowed to take custody (the exact noble to decide depends on how far spread the Imperial Citizen's crimes go; if crimes are lodged on Regina/Regina and Terra/Sol, it would take a ruling from the Emperor to decide who received jurisdiction, as the crime was trans-Domain).
3-Member Worlds are entitled to defend their world. They are granted Local Naval Jurisdiction out to 100 Diameters of the surface of their world, the world's Inherent Defense Zone. Member worlds may apply for and be granted the right (by the Sector Duke or above) to take jurisdiction over the 100 Diameter zone of other worlds within the same star system. If a Member World has control of a world in another star system, it may also apply for and be granted control over that world's Inherent Defense Zone. Member World naval vessels may not equip jump drives unless they have been granted the multi world control waiver noted above, in which case they may further apply for per-ship jump equipage waivers (the local Sector Duke would decide exactly how many ships to allow to equip jump drives).
4-Member Worlds are entitled to be defended by the Imperial Military, as judged necessary and expedient by the Sector Duke and Sector Admiral (and possibly higher authorities, in some cases). (Note: Except in the case of general war, this means that a world will be defended against any attack.)
5-Imperial Citizens from each Member World are permitted to conduct trade throughout the Imperium with the sole exception of Red Zone worlds. No Member World may establish any form of taxation, duty, tariff, etc., against any other Member World that is not levied against all Member Worlds evenly.
6-Each Starport managed by the Starport Authority Bureau of the Ministry of Commerce is Imperial Territory, both ground and orbital facilities. Imperial Law applies fully in this Territory. Non SPA Starports must adhere to all Imperial Law regulations regarding safety, traffic control, storage of goods, and legality of goods (overseen by SPA regulators).
7-The Imperium may purchase territory on Member Worlds, and if it does so, this territory is Imperial Territory. This applies to Starports run by the Imperium, Ministry Offices, Noble Offices, Military and Scout Bases, etc.
 LMWA, Duties and Restrictions
1-No world may succeed from the Imperium under any circumstances, for any reason or cause of belief.
2-The Imperial Human Rights Accord must be observed. (1)
3-The Imperial Rules of War must be observed.
4-Imperial Criminals must be extradited to Imperial Jurisdiction.
5-Imperial Citizens are allowed freedom of movement off their homeworld. (2)
6-Any Imperial Citizen may attempt to enlist in any Imperial Service at will, and no Member World may block this under any circumstances. (3)
7-No Member World may form any type of political or military alliance between themselves and any other Member World or domestic organization, or any foreign nation or organization. (4)
8-The Imperium and its hierarchies are the Government of the State, and no other may supplant it. (5)
(1) The Imperial Human Rights Accord was one of the primary incentives used to persuade planetary populations of candidate worlds of the worth of joining the Imperium.
(2) Access to offworld travel cannot be made impossible by regulation, obfuscation, or trickery. A handful of extremist governments use propaganda to persuade their populations that leaving is a bad idea; some even use regulations to make it difficult, though as noted these difficulties cannot be so extensive as to render leaving effectively impossible. I3, the ISS, and the local Ruling Nobility (and their appointed Officers) conduct observations to assure that this rule is obeyed.
(3) The Imperial Services are under no obligation to accept unsolicited job applications, though, and can turn away anyone they don't need. Condition 5 is a requisite for Condition 6, and if this were not the case, there would be insufficient personnel to fill the positions of the Imperial Government (most especially the Navy, Army, and Marines).
(4) This does not stop Member Worlds from owning other worlds wholesale, though, in this case, it is not an "alliance", but rather outright extension. In some cases, Member Worlds were originally admitted to the Imperium as a cluster, with one world effectively governing others (Captive Government). However, as the centuries grind on, most worlds subject to such governments tend to form revolutions to throw off such governance, and as long as the conflict does not escalate beyond certain parameters, the Imperium will not interfere. LMWA Freedom #4, though, usually prevents the reverse, as Member Worlds under attack by another may request protection from the Imperium (and that the Imperium has a much tougher time ignoring).
(5) No Member World may establish any organization that supplants the functions of the Imperial Government, or otherwise attempts to overtake the responsibilities that fall upon any part of it.
In all cases, the Imperium reserves unlimited rights to intervene in a Member World's affairs if the government violates these rules, or if they cannot prevent their citizens from violating these rules on a consistent basis. Intervention may take many forms, where military intervention by the Imperial Navy, Army, or Marines is a last resort. Intervention usually comes first in the form of the local Count ordering the world's Margrave take up a mandatory advisory role to the planetary government, a limited command authority role, where the government must follow the advice (suggestions, orders, what have you) of the Margrave in matters related to correcting the violation; protests by the planetary government in favor of alternate plans are moot at this point, if the planetary government's (or one of them, in the case of balkanized governments) previous plans to solve existing violations worked, the Count would not have had to order the Margrave to take on the direct command role. If the Margrave's advice (orders) is refused or cannot be carried out for whatever reason (reluctance, incompetence, etc.), then Imperial Interstellar Intelligence's Intervention Branch personnel are called in to implement the Margrave's advice (in whatever reasonable form the Margrave requests). If violations continue at this point, it is usually the result of active opposition. I3 can, at this point, bring in additional assistance in the form of a small army of operatives. If military opposition to violations corrections arises, then the military is called on, although the Count and Duke will view this as a failure both on the part of the Margrave and I3. In practice, results rarely escalate to the point where a Margrave is ordered to dictate to the planetary government, most such governments are well aware that opposing the Imperium is generally pointless, as so much mass can be brought to bear against them that their opposition will probably fail. Eleven hundred years of success in these matters, and the usual political education of the planetary government's rulers (during childhood, etc.), helps them to understand this. It is usually when the poorly educated claw their way into government, those who lack an appreciation of the strength of the Imperium when the mass of its power is brought to a point, or whose background makes understanding the scope of the Imperium in comparison to one world either difficult or impossible, that situations may escalate to serious levels.
Violations of the Imperial Rules of War bring more severe reactions, depending on what was done. The Imperial Navy will take immediate action without consulting anyone if it learns that any agency anywhere in the Imperium other than itself is operating, in possession of, constructing, or planning to build any Strategic Weapons System without explicit authorization from the Emperor, and after the action is ordered and underway, will then inform the appropriate parties (reports will be created and sent off within twenty-four hours), which include the Count, Duke, Archduke, and Emperor, plus I3 and the ISS. In cases where conventional military action reaches a scale where it becomes a threat to the Imperium (a decision resting with the local Count), appropriate local parties (Count and Duke, plus I3 and ISS) will be contacted and planning for appropriate (overwhelming) intervention will commence (and if the planning proves unnecessary later, it turns out to be good training). Imperial Navy elements are assembled to escort assault transports full of Imperial Marines (and, if necessary, Army units) to the target world. This usually ends the problem, quite messily.
