I think it's more akin to the first option, myself. If you can fit a few battalions or even brigades inside a massive capital-class vessel anyway, why risk putting them all in a more vulnerable troop-transport? I envision troop transport in the Firestorm universe as something akin to Starship Troopers: the Rodger Young was a combat ship, if I recall correctly, but the troopers themselves deployed in drop pods straight from there to the surface. At least, that's my recollection--but it's been about 15 years since I read the book, and even longer than that (thankfully) since I saw the movie.
So that begs the question: how many drop-pods can a battleship in the Firestorm universe deploy? And how do the troops and equipment get back? Not sure if we'll ever see answers to these questions.
I could also see them having another option--some sort of armored transport that deploys from cruiser/battleship-rate vessels, for invasions on planets where drop-pods would be ill-advised (stormy atmosphere, atmosphere too thin to stop the pods from smashing into the ground, too much vegetation, etc).