A "happening" Hellraiser refers to is
here.
My views are:
(a) you can't reliably store a single item in multiple transport bays simultaneously because there could be walls between the bays. This doesn't exclude the possibility of being able to do so on specific designs, but it doesn't seem like the kind of thing you can plan on. For ASF/Small craft bays, even that may be disallowable due to pressurization concerns: you don't want to evacuate an entire hanger just to launch one fighter.
(b) For dropping, you need to use a drop cocoon which plausibly requires some significant extra space, so it makes sense to disallow it.
(c) For launching, I'm hazy on exactly what happens to air pressure in the transport bay. Is it the door which functions as an airlock or the transport bay? If the latter, cargo which can't withstand some vacuum could have a rough time. At the same time, disallowing launching while allowing disembarking seems inconsistent. I'm also quite skeptical about the thought of igniting fusion engines _inside_ a dropship under any circumstances. That sounds absolutely disastrous. More reasonable is having an EM catapult shove an ASF into space, and then starting the engines. And an EM catapult launch doesn't seem to require appreciably more space/allowances than disembarking.
(d) W.r.t. other units in bays as cargo, it seems reasonable enough---plenty of garages can elevate a car into storage for example. Gameplay wise it also seems good as it gives a significant boost to the desirability of small units, and it makes you start thinking about combat force per ton rather than combat force per unit. That's generally good for a game since it makes many more potentially good solutions.
(e) There's a separate issue about the 'realism' of Small craft bays. It is somewhat odd that ASF bays have a 50 ton overhead and give transport bay life support to 2 while Small craft bays grant transport bay life support with a 0 ton overhead. If anything, Small craft bays should have more overhead, since Small craft have significantly more varied form factors.
Anyways, I flagged Hellraiser's question for notifications---it will be interesting to see how it turns out.