Combat skills on the player's flagship can only be gained by the player getting Combat skills, and can not be gained through officers.
If officers offered access to fleetwide skills, then they would in fact grant you access to something that's equivalent to spending skill points. (Unless the fleetwide bonuses from officers were different, etc etc.)
So, it's not at all an equivalent situation. Whether Combat skills end up being "worth it" or not is a balance question, and, as you say, player skill also factors in (though arguably, combat skills can be even more important for worse pilots). Officers offering fleetwide skills is generally not a balance question - it just makes the player picking those skills themselves a bad choice, regardless of relative skill power levels. (I mean, you could also try to balance it by say having an extreme salary cost or something, but there's still a qualitative difference.)
That's really all I'm saying here - design-wise, those two things are vastly different.