If you do a save game with arbitrary names, the engine should check if it might overwrite existing files (and then prompt) and probably make sure the extension is .sav.
I tested Requiem, Quakespasm, Fitzquake, Darkplaces and FTEQW with this.
Fitzquake and by extension Quakespasm are affected as is Darkplaces. FTEQW fails silently and Requiem saves as pak0.sav.
Quakespasm's output on Linux:
and on the next start:]save pak0.pak
Saving game to /home/me/.quakespasm/id1/pak0.pak...
Please always append .sav to savegames if the user-supplied name does not already end in .sav!QUAKE ERROR: ./id1/pak0.pak is not a packfile
edit: I hope it is clear that this affects all commands/cvars where filenames are supplied by the user or server!