I think that the rules as set out in High Guard are reasonably clear cut. Exactly how we interpret the reasons for these however is another matter.
In the first place small craft are assigned tonnage equal to their own size on ships of 1000dTon and under and at 130% of their tonnage on ships of over 1000dTon. Exactly why this is, is open to endless debate. I have always considered it more as a move to retain basic compatibility with the earlier Book 2 design sequence in which all small craft were carried at their own tonnage irrespective of the size of the mother ship rather than for any technical reason. Also, remember that Flight crew are not a regular feature of ships below 1000dTon as the High Guard crew rules don't kick in until over 1000dTon so it could be argued (and this is an interpretation nothing more) that the additional space on ships above 1000dTon is more to do with the presence of a flight control facility or possibly the requirement for military stores of spares etc associated with the maintenance of the small craft.
Large craft are carried at 110% of their tonnage on all mother ships irrespective of the tonnage of the mother ship. Why is this? I can't say, after all I don't design starships for a living. However there is no need for this to be backwardly compatible with the Book 2 sequence since although there is no explicit prohibition there is also no mention of the possibility of carrying larger non-starships or even starships in the Book 2 design sequence.
There is no get out for the use of these displacements other than the sub 1000dTon rule for 1000dTon and under mother ships. The issue of hull configuration does not influence the allocation of tonnage. This in some ways leans towards, but in no means proves correct, my assumption that the additional space is due to a flight deck/control facility or stores and maintenance space.
Launch facilities are a different matter, and High Guard does appear to contradict Supplement 9 in this area. Three launch conditions are specified.
Dispersed Structures (Hull Type 7). High Guard explicitly says that these vessels carry craft and ships attached to their exterior. They need no additional fittings. All craft carried by a Hull Configuration 7 ship may be launched in one turn.
Launch Facility. The de facto standard for most ships where a single craft or ship is launched per turn per 10,000dTon of mother ship. No additional displacement and no additional cost
Launch Tubes. Displacing 25 times the tonnage of the largest vessel to pass through them at kCr2 per dTon of tube capable of launching 40 vessels per turn.
Supplement 9 lists only 2 Dispersed Structures, the 400dTon Survey Scout which would be in the sub 1000dTon classification and carries only one modular cutter with two modules (presumably one is installed and one is ready to be rotated in following some maneuvering). The other is the aforementioned 50,000dTon Arakoine Strike Cruiser. This carries 100 heavy fighters and has 2 launch tubes implying the presence of a hanger deck rather than carrying all the fighters on the outside of the ship as suggested by High Guard. Arguably with the exception of the nose arrangements this vessel could be considered a close structure, whilst the Wind Class 75,000dTon Strike Carrier is possibly more dispersed in some peoples eyes.
I'm not sure that this actually impacts greatly on the design sequence, it is more of an issue for the deck plans. In essence the design decision comes down to whether or not to install launch tubes, and based on Supp 9 a dispersed structure can have these as well as any other configuration, and in this respect this does not actually contradict High Guard.
If no launch tubes are included then the launch rules for standard facilities should apply in combat except that when a dispersed structure is noted to be carrying the ships or craft externally when a rider can be added allowing it to launch and recover all externally carried craft in one turn.
As always others may have a different view.