I feel your pain for sure. Have you tried using Simple Quake Launcher tho? My Quake directory is at least 4Gbs maybe more. But I have not had to look at it in a while. With SQL you can choose engine, game (Quake, Quoth, Hipnotic etc) then game directory, map and skill level and then command line switches. It's helpful.
Now this won't completely solve your problem and I am seriously considering the same thing you are talking about BUT SQL has made things much easier to launch and switch back and forth between engines. MarkV does mess up your config but I just save mine to a custom and exec from there. There are only 2 drawbacks: it defaults the gametype alphabetically so I have to change 1000 to id1 etc. and it takes a while to load becuase it scans your Quake directory on launch.
I really like it a lot. Give it a shot.
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