Realistically, the in universe reasoning for the size of the newer ships makes sense to me. The FO controls a lose collection of planets... but also needs a place to house their military while on campaign, and invading worlds means a lot of infantry. The Supremacy is massive because its also a shipyard that can build and repair ISDs and RSDs. The crew for those would need to off load during repairs as well.
So the size is a combo of, fewer worlds to occupy and house troops thus needing to keep them somewhere (on the RSDs).