There is one thing that nags at me: runabouts as part of a starship's complement of attached craft.
I keep thinking, "Don't these things belong to starbases, outposts, and the like?"
had a runabout in "Timescape" and some of the comics. So it's canonical that runabouts can be support craft for starships as well as starbases.
Which couldn't have been a temporary loan-out to the Enterprise
whilst en route from one home base to another?
(Remembering that this particular Enterprise
has dropped off runabouts to bases like DS9.)