As for commanders commanding Star Ships, are there really any examples?
Depends on what one considers a "starship".
A man wearing two solid braid commanded the transport
Antares for Starfleet in "Charlie X". We never learned what his rank was, but it would be awfully confusing if his two braid didn't mean Commander exactly like the two braid on Kirk's top officers did. But the
Antares wasn't much of a starship, apparently, and only had a crew of 25.
Of course, the blouse worn by the skipper of the
Antares had earlier been worn by Kirk in the pilot episode "Where No Man". So we could argue that Kirk held the rank of Commander in that episode, despite commanding a mighty starship. Or we could argue that the rank system was subtly different back then (even though various spinoffs have hence supported the idea that two solid braid meant Commander long before TOS). But it would make no sense for this putative older rank system to remain in parallel use with the modern one in "Charlie X".
Various people with three pips or less commanded the
Defiant on several occasions, including Cmdr Sisko, LtCmdr Dax, LtCmdr Worf and even Major Kira. But again, the
Defiant isn't much of a ship, and apparently only had a crew of 40-50.
Various low-ranking people have been seen in command of both our hero ship and various large guest ships. Those have been temporary commands, though, or at least have never been proven to be permanent ones. For example, one LtCmdr Hobson was the ranking officer aboard the giant
Sutherland in "Unification II", but that doesn't mean the ship's regular skipper would have had fewer than four pips, as it was made explicit the
Sutherland was dragged into action from the middle of a refit. Similarly, a mere Lt(jg) was on the center seat of the similarly gigantic
Prometheus in "Second Sight", but this doesn't mean the ship's proper CO wouldn't have been a full Captain.
Timo Saloniemi