Yes, Combat is comfort tree. The only Combat perks I see truly vital are Combat Endurance 1 for more peak performance (and mitigate the pain caused by overly cowardly AI) and Helmsmanship 3 (to allow zero-flux boost when fighters are engaged).
As I wrote before, a problem with some pilot-only skills - in all non-Industry aptitudes - is they marry your character into a ship, and Starsector is too long a game for that to be enjoyable.
The idea of your player being an administrator, while his officers are pokemon who he can choose one for his combat flagship can be a solution to that.
EDIT: Or player could be combo officer and administrator. In theory, he is already this. In practice, he does not have enough skill points to pull it off, thanks to empty aptitudes sucking at least nine skill points away, and if you get enough buffer and/or campaign comfort skills, you do not have enough skill points left to match level 20 officers in combat. Plus, if you want to be the best pilot for a given ship, you will be married to it like a sword-and-board fighter with weapon specialization skill/feat chain is married to his longsword.
Currently, ALL of my characters have the following skills:
Combat: Combat Endurance 1, Helmsmanship 3
Leadership: Fleet Logistics 3, Coordinated Maneuvers 1, Fighter Doctrine 3
Technology: Electronic Warfare 1, Loadout Design 3
That is 24 out of 42 points spent, leaving 18 left for everything else. That is not very many points left, for less personal skills than what level 20 officers get, even if I completely ignore campaign comfort stuff like Navigation or anything from Industry; not to mention if I want Industry, that is more points wasted on a empty aptitude.