Yagami Quake 2 works.
I installed Quake 2 a bit differently than your instructions. I'm running Linux Mint 17.3 Cinnamon 64bit.
I had an issue with the command line: innoextract -d output setup_quake2_quad_damage_220.127.116.11.exe
Kept getting "-d" 1 errors" or " d 1 errors".
I used Wine to install Quake II Quad Damage (GOG) and copied all the files over to the Yagami Quake 2 folder (even over writing some in the process). Then, I uninstalled Quake II Quad Damage. From there, Yagami runs all the Quake II games flawlessly.
I've since created a zip file of the fully functional Yagami Quake 2 game and backup copied it to my external hard drive for safe keeping (the whole point of DRM-free).
You've got one Hell of a good Linux source port there. As a new Linux user (as of a year ago), I greatly appreciate it.
Hmm a bit strange, I just tried the command myself and didn't encounter those issues. I'm glad you got it to run though, it's a really great game.