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The command line arguments for the Mission Packs are wrong in GoG.

They are currently "-game hipnotic" and "-game rogue", but should be just "-hipnotic" and "-rogue". If you use the later, you will get the Mission Pack-specific modified ingame status bars and map options when creating a multiplayer game.
Interestingly, Armagon CD has ARMAGON.BAT which runs the game as:
c:\quake\quake.exe -game hipnotic -hipnotic
while Dissolution .BAT files run the game using '-rogue' only. Its MANUAL.TXT also says this:
Note: You must change to the directory where Quake is installed (i.e.,
c:\quake), then from the command prompt run the following commands.

Single Player: quake -rogue
Dedicated Server: quake -rogue -dedicated # +map start
Listen Server: quake -rogue -listen #
So maybe the safest method is to use both '-game hipnotic -hipnotic' and '-game rogue -rogue' just in case.