I'm still not sure of the pros and cons of them being at least semi-independent (up to RADM or even VADM but still answerable to the Commander, Starfleet and potentially the Chief of Starfleet Operations) rather than them being totally interchangeable with regular Starfleet Exploration Division/Deep Space Exploration Corps personnel?
I don't think there would be a separate high-level organization. Since Starfleet seems to be organized regionally anyway, I would imagine ships for shorter-range missions would be under a squadron (or whatever) commander who reported to the local Starbase commander. A possible model might be USN PT boat squadrons in WW2, which were designated coastal forces under local Sea Frontier commanders. PT boats that went into forward areas without bases were accompanied by a tender. A similar arrangement was used for patrol boats in Vietnam.
I tend to blame things like that on budget more than anything else. Not really any other good reason for most Trek battles to be stuck in three-dimensional World War I naval tactics at best.
Or earlier; even in WW1 battleships normally fought seven to ten miles apart!