Voyager has no commander's, only one Lt.commander as it's first officer and a full lieutenant as it's (de facto) second officer
According to a casualty list glimpsed in "Imperfection",
Voyager prior to that episode lost at least one Commander and two Lieutenant Commanders in addition to Lieutenant Commander Cavit. It seems fair to assume that all these high-rank casualties were suffered when the Caretaker wave hit the ship. Supposedly one of those casualty list Lieutenant Commanders (either Ziegler or McCarry) was the Chief Medical Officer we saw but didn't hear named, while the other one might have been the Chief Engineer. If the novels give another name for the CMO, then that's four known LtCmdrs aboard that ship in "Caretaker"... The Commander (Bartlett) was probably the Chief Science Officer or somesuch, set aside from the direct chain of command and thus not at odds with the fact that the XO was a mere LtCmdr.
So the Starfleet way of crewing the
Voyager need not be at odds with how the
Titan is crewed, or how the
Enterprise-A ended up being crewed eventually. The later Janeway/Maquis way would of course be different.
As for Gomez' yellow uniform vs. Admiral Toddman's, I'd argue that Admirals come in all colors. If we ever saw the top Medical or Sciences Admiral, he, she or it would be wearing blue. It's just that the plots never feature such flag officers, because the plot function of an Admiral is to give (hated) orders to the hero Captain, and only the "Command color" Admirals would have an excuse for doing so.
Toddman might have represented Starfleet Intelligence, a department whose colors are unknown to us. Usually SFI deals with hero skippers through intermediaries, typically redshirted Admirals. But Toddman might have been a rare direct contact with SFI.
Would Captains represent the full spectrum in a similar way? The novels don't exactly preclude hundreds of science vessel skippers from wearing blue. They only establish that there are no skippers who would represent the "yellow professions": Security, Engineering, possibly Intelligence, perhaps others. Which sort of makes sense: Security would not have its own starships, but would rather operate humble police cutters (if any) for purely Security-related jobs. And there would be few Engineering ships; most of the repair vessels or tenders out there wouldn't require a skipper who knows about engineering, and arguably the
da Vinci doesn't/didn't, either (Gold always wore red, right?). As for specialized Intelligence vessels, I doubt the color of uniforms worn aboard those would be common knowledge.
Timo Saloniemi