My current thinking is to have three types of troop transports bays: standard, orbital insertion and ship-to-ship boarding, all of which have capacities in tons. Standard is similar to the current troop transport bays, where loading and unloading takes several hours or days. Orbital Insertion Bays have abstract drop-ships built into the transport bays (significantly more expensive and a little larger than standard bays). Orbital Insertion Bays can be used as normal troop transport bays, with normal load and unload times, or they can be used to instantly drop troops on to a planetary surface from orbit, in which case the bay is damaged and has to be repaired by a shipyard (replacing the abstract drop-ships). Ship-to-ship boarding bays can also function normally, but have a secondary function for launching infantry units (with boarding capability) against other ships. This doesn't damage the bay. Standard Bays would be commercial, while the other two would be military systems.
Part of me likes the ability to have dropships as small FACs that can launch for the final million kilometers of the trip so the troop transports don't have to risk defense fire, but thinking about it your way is probably better. Less micromanagement that way, since you don't have to offload the troops from the transports to the dropships manually.
I had one thought, and it's kind of a biggy. As long as we're treating the troops and dropships as basically launching from hangars... would it be worth considering making space fighters and aerospace fighters the same craft? So that, say, carriers could use their fighters as part of the ground landing, and a planetary garrison could launch their fighters into space to help in the defense?
One way I could see doing it would be to just give planets an effectively infinite hangar capacity, but only for fighters (though unlike when in ship based hangars, you'd be paying maintenance on them like I assume you do for ground troops, so it's not as unbalanced as it sounds). Then fighters engaging in ground combat would still have their stats based off of their components, but maybe with an accuracy bonus compared to orbital bombardment for the weapons.
If I understand correctly, right now there's a divide between aircraft and space based fighters, which makes sense from a technical perspective. But fighters being able to enter the atmosphere is kind of a sci-fi staple, and it gives beam fighters an interesting role as hybrid space/ground units.