If you look at the administrator "Anne Kokawa", she obtained the pain resistance skill when i increased her aerospace skills. But in the campaign options, i have pain resistance set to requiring the Piloting/Mech skill. It looks like auto generated special abilities (given when the skill level reaches veteran or elite) are ignoring prerequisites set in campaign options.
The same thing also happens to randomly generated personnel in the personnel market. The following special abilities are also ignoring prerequisites (taken from the rules spreadsheet) :
Weapon specialist : May only be generated for weapons on the assigned unit, but can generate with ANY value...you can have conventional infantry generated with weapon specialist : medium pulse laser in 3025 for example.
Laser/Missle/Ballistic specialist : May only be generated if the assigned unit has that particular weapons type, but may be generated with no prerequisites, you can have a LRM carrier gunner generate with laser specialist for example.
Hopping/Jumping jack : Should only be generated if the assigned unit has jumping MP.
Melee specialist : Should only be generated if the assigned unit has a melee weapon.
Oblique attacker : Only if the assigned unit has LRMs or artillery (ASFs should not be allowed to generate with this as they cannot perform indirect fire anyway)
Save file contains an example of an infantry unit in the personnel market being generated with weapon specialist for a mech scale weapon which shouldn't be possible.
Maneuvering ace : Unit with at least 6+ walking speed
Sniper : mech with long range weapon
Some of this may be an AtB issue, but I have noticed this problem more generally when hiring new personnel. Sometimes they get SAs that make no sense given their skill set and role.
I would note that I don't think the generated abilities should be limited by the current unit assignment as this may change and pilots may be hired without an assigned unit directly.