[...] imagine Counselor Troi commanding the Enterprise even though Data is the more capable in a crisis situation.
By the end of TNG, that seemed to be inexplicably a possibility. After passing her "Bridge Officer Examination," Troi was promoted from Lieutenant Commander to Commander, while Data - who had been out of the Academy for 25 years, compared to Troi's 11 years, and was Chief Science Officer, Chief of Operations,
and Second Officer of the
Enterprise-D - was still only a Lieutenant Commander. Yet was Troi really qualified to be in command of the ship compared to Data's qualifications and experience? I'd think not, but if a crisis situation arose wherein Troi was the ranking officer on the bridge, command would have fallen to her by default even if the ship's Second Officer was there too!
After Janeway died in Before and After "someone" awarded Chakotay four Pips to demonstrate that his Captaincy was real...
This was odd, too. While Chakotay could certainly be captain (position), there was no one of sufficient standing available to promote him to Captain (rank). The death of one's captain does not automatically promote the First Officer to Captain (rank); the First Officer (or highest ranked remaining officer) would only assume the position of captain. Only an officer of flag rank would be able to promote another officer to Captain (rank). If an Admiral had not promoted Chakotay to Captain, then Chakotay would have been guilty of illegally assuming a rank that was not his. Of course, looking at Memory Alpha, it appears that the timeline in "Before and After" in which Chakotay was Captain of
Voyager was set in the year 2379, which would be 3 years after Project Pathfinder established contact with
Voyager in the proper timeline, so it's certainly possible that Chakotay was promoted to Captain via subspace orders from Starfleet if Pathfinder was successful in that alternate timeline as well.
Was Chakotay the XO because he was the leader of the Maquis or was Chakotay the XO because of his awarded hypothetical and imaginary rank? What if their was a power struggle inside the Maquis that by their traditions Chakotay fell from Grace? Would he accordingly lose his position of if he was no longer representative of the ruling body of the Maquis?
Somehow I doubt that Janeway would've accepted any other Maquis - except perhaps B'Elanna - as First Officer, regardless of any internal power struggle within the Maquis onboard
Voyager. She probably wouldn't have tolerated any internal Maquis political struggle, anyways, since she expected the Maquis to act as Starfleet once she issues their provisional ranks.