hi Daiwilletti,
this is a pretty interesting question and I am sure someone tried it already, I never installed WOFF, BOB, MAW or such big CFS3 game overhauls, maybe there is it solved.
the stock pilots are loaded from a CFS3 "library", if the airplane gmax project contents a Pilot node (which is basically axis point where he should be placed). but our own airplane pilot character means it is simply another 3d object hardcoded into the external airplane model interior, it is unmountable.
by my guess it could be theroethically possible to globally replace or to add new character m3d file (see the "Combat Flight Simulator 3\characters\" content and/or to edit the related xml files (unlimitedpilots.xml, country.xml). they seems are the in-airplane sitting static figures.
I dont know from where are loading the ingame motion catpure rigged (animated) characters, but such ones we really cant do I suppose.