Some copies of the id Anthology version contain an updated Final Doom; the rest uses the original. The GOG.com release uses this alternate version.
All patches for the retail versions of Final Doom (as well as Doom and Doom II: Hell on Earth) can be found here.
The following lists source ports that supports borderless fullscreen windowed, either natively or though third-party programs.
Run the program as administrator
The yellow keycard in MAP31: Pharaoh from TNT: Evilution is missing due to it being accidentally flagged as a multiplayer-only item, making it impossible to complete the level with 100% completion without resorting to cheats.
DOOM2.EXE -file TNT.WAD TNT31.WAD
DOOM2.EXE -file TNT.WAD