My take: Baltar had an identical "Lords of Kobol" medallion as Adama, allowing him entrance to the Kobollian tomb in "Lost Planet of the Gods". Baltar also appeared to be an active member of the Quorum of the Twelve (also, along with Adama). While not stated specifically in-dialogue, I would take these things (along with the "caught between the President's battlestar and my own" comment) as evidence that he was, in fact, in charge of his own battlestar.
Sadly, due to bad writing in places, we have some weird things happen later on - We know there were multiple fleets of battlestars, as evidenced by the Pegasus being the flagship of the "Fifth Fleet" ("Living Legend"), explicitly implying that there were at least four others, probably more. Commander Cain was NOT a member of the Quorum of the 12, yet commanded his own battlestar (Pegasus), of which there were assumed to (also) be 12 (one per Colony). Plus, we also have Commander Kronus ("Take the Celestra") who dressed similarly to Adama, had once commanded his own battlestar (Rycon), but also NOT a member of the Quorum of the 12, so membership on the Quorum does not imply leadership of a battlestar. Unless it
did, in which case there would necessarily need to be more than 12 battlestars to allow Cain and Kronus to fit in that command structure.
As for the Cimtar fleet of five battlestars detsroyed in SoaSW, I would call that the "First Fleet" in my own head-canon, only assembled when the President needs to be transported somewhere for an event of extreme diplomatic significance to the Colonies, as you likely wouldn't have that many capital ships moving together and all at once without ANY escorts, in what we would normally consider a "battlegroup" in modern military parlance. I would have considered the alliance between the Colonies and the Delphian Empire against the Cylons to be one of those important events to have the "First Fleet" mobilize to a signature ceremony at some neutral location between political borders. To this end, I would consider a Colonial "fleet" consisting of a maximum of two battlestars, with escorts, cruisers and destroyers to accompany them. In the apocrypha, there were said to be only 12 battlestars, which would compose 6 independent fleets (Fleets 2-7), and the one, hardly-ever-assembled "First Fleet" for high-profile presidential operations. There is so little known or developed about any of this, there was a lot of room to imagine how something like this would work without getting too weird about it.
I liken this to Trek's Constitution-class uniform insignia debate. They threw some random things in there in an effort to supplementally world-build into interesting stories, got production staff (costuming, VFX) involved to build corresponding visuals, without realizing that they were introducing some hidden inconsistencies that
nobody ever envisioned would be picked apart and scrutinized by fans like us decades later. BSG is full of such things. So is RDM's BSG, but to a lesser degree, particularly as it applies to rank device and prop usage.
In any case, I find it fascinating, and BSG is one of my all-time favorite shows (both versions).
