..something as small as a runabout is considered a "ship."
Sure, it pays off to do that when said runabout is the only Starfleet asset within 70,000 lightyears (such as in "Vortex" which IIRC is the only episode to use such terminology). In the context of 600-ship formations, things might be a bit different.
Fleets being non-permanent structures is a reasonable idea that carries some connotations. We hear of Fleet numbers up to 10 in DS9, but not 1st, 4th and 8th or anything higher than 10th. It's statistically very unlikely that there would be Fleets with numbers much higher than 10, then...
...And also rather unlikely that 1st, 4th and 8th Fleets would not
exist. After all, the gaps in the current USN fleet scheme are due to there being a permanent numbering scheme that covers peacetime conditions and the existence of shipless Fleets. If Starfleet Fleets only come to being during wartime, it wouldn't make sense to leave out any in-between numbers - especially as we have seen that a specific number does not correlate to a specific mission or theater of operations, but merely accompanies the formation as it dashes from one assignment to another.