I still have yet to find any good reason for why they disabled this. "Causes problems in multiplayer mode" is not an answer. Does it make your client crash occasionally? Are their weird video problems? These are all things that it should be up to the player to deal with if they so choose, a hardcoded "no windowed mode" is retarded when the original game itself supports it fine, and other mods also support windowed mode fine, multiplayer or not.
Is there any chance that the CF devs might bring windowed back to FL? I can't play it in fullscreen because FL doesn't seem to play well with dual screens, and alt-tabbing makes freelancer crash more often than not.