Well, final tally of compatibility errors I found when testing QF on Beta 6:
1. Certain textures (large trees, sky domes, etc.) are missing. (Yay rainbows!
) Possibly fixable... silly old power-2-size!
2. Mission 11 (S&R finds you near a large 3-way air battle, escort engineers, protect dropship,) did not finish properly. Once the dropship is repaired, you are ordered to get inside for takeoff. I got in; it never took off. I assumed that was the end of the mission: "game.cheat bzwinner"
Those are the only problems I ran into. Problem #2 may be specific to my computer; I've had similar problems playing FE. Other than that, GREAT compatibility!
NOTE: I have not beaten bonus mission #2 yet, due to INSANE difficulty. (That stupid engineer taking the wrong turn EVERY time!!! lol) Thus, I have not played through ALL the missions yet. If there's a problem with the bonus missions, sorry. I didn't get there.
EDIT: I finally beat the second bonus mission. No errors.