Remember, too, that some of those crazy routes may be there for purely political reasons. There may also be some routes that bypass system A (Importance +3) in favor of system B (Importance +0) because 300 years ago system B was Importance +2 and system A was Importance -2.
One of the things I've never seen discussed in canon, and only discussed here in broad details, is how the x-boat routes are changed.
There are three interrelated factors here:
Trade will go where the markets are. So as worlds become more important by increasing trade (and population) the trade routes will shift. Conversely as worlds loose population or fall behind, the trade begins to dry up.
The second is the Imperial Nobility. In the T5 rules and Imperialines rules, each of the Nobles above the rank of Knight will have holdings somewhere outside of their demesne. In theory (nothing in canon contradicts this) a noble could move their demesne to any of their holdings. There are examples in canon of nobles moving their capitals around.
The third is the x-boat routes. Technically these are controlled by the IISS. But as several people have pointed out, the routes must be at least influenced by politics. If you move one endpoint it would have effects across an area the size of a subsector. So moving a route would, with the cascade effects, be done after consideration and consultation with all the affected parties. That is, very rarely.
This is generally in the order of effect. The political and trade situation on various worlds cause the Imperial nobility to follow along, which forces the IISS to update the trade routes.
There are cases where changes in the Imperial nobility situation is cause of these changes. A canon example is in the T20 Gateway domain with the replacement of the Archduke. The capital is moved, everyone goes with them. Or in GT:Rim of Fire where the Archduke moves the capital for reasons of local politics.
The problem with mapping these changes over time is the precipitating events are not predictable. Important people dying without heirs, political revolutions, wars, natural disasters, and so on. I know both the World Builders Handbook and the T4: Pocket Empires have tables of events of these sort to make your colony and empire more interesting.
Having some agreed upon rate of change for these things would make mapping these changes easier. On a sector scale there would be minor updates to most of the worlds (population changes mostly), with a more major event on 1 out of a hundred worlds (TL or pop digit adjusts, government changes). This would change the trade routes. These changes may precipitate a minor realignment of nobility (a count or baron moves their demesne).
Once a decade the accumulated changes cause a more significant realignment (Count or duke). Which may or may not push for a subsector level change in the x-boat routes.
The problem with the T5 Second Survey data set is the Nobility is all accurate according to the rules. But in a real, dynamic, universe there should be a visible number of violations of the rules. As people have pointed out with the existing x-boat routes. But both requires a know history to explain.