Can I split battalions into companies for transport like that? Or am I fine if they're in the same task group?
Yes you can... I think (in the same tg). I believe I did that in a previous game (for the construction brigades) but the last few versions I have gone the giant troop transport route.
Just in case this wasn't clear, I mean a drop ship for planetary assault not for like ship boarding.
Multirole, you can use it for either.
My alternative is a 16000 ton destroyer with a ton of armor and shields and 6 cryo drop pods (whole brigade plus div HQ or replacement battalion), which would replace both ships.
This is also a good idea. This is what the UNSC in the Halo universe handles it,
EVERY ship doubles as a troop transport.
and as far as I can see theres no other company sized ground units.
Ship boarder defense and RP.