I get the analogy, but Chief Engineer on a starship surely must be closer to rocket scientist than boat mechanic. Or at least equal parts mechanic and physicist.A chief of security who is also secretly part of section 31 would seem like someone who should be more qualified than a boat mechanic to be 3rd in command.
I agree with your point though, Reed would have made more sense than Trip.
And we see folks in red who are in command of nothing as well - conn officers and the like. There's also one instance of an Admiral in gold. Beverly Crusher is also a command-grade officer and she still wears blue too. The problem with having so many jobs and only 3 uniform colours is that lots of jobs get lumped into the same 'box' that don't necessarily belong together. The colour of your uniform doesn't necessarily denote your ability to command, just what your 'day job' is.However, there's obviously a hole in this theory because Troy took the command test but never ditched the blue shirt (when she chose to wear a uniform).