Hello. I spent some more time on this over the holiday weekend and I discovered that "apt-get remove -y" seemed to be causing the system to hang in the script file but "apt-get install -y" was not. I sort of "solved" this issue by having SimCity 3000 run the install command in it's start script and the MUGEN games run the removed command in their scripts.
I also found that I had to end the install command with "&" for the script to proceed without significant startup lag. But, strangely, I could not use the same trick for remove command - even though that should theoretically take less time since it's not downloading anything. Morever, I had to end that line with "&&" or else it would never go past the launch screen. (This may be what's actually preventing the remove command from causing an endless hang.)
Anyway, this all nearly solved this issue -- except the MUGEN games still throw an error screen in the Wine Desktop upon their first launch after running SC3K -- the same error you would get if xserver-xorg-video-fturbo was still installed. So it seems like the remove doesn't "take" until after the second launch. (Right now, you need to exit out and re-launch, after which it will also work. And you can only exit out with the controller since I use xboxdrv to remap the controls prior to launch.)
Anyway, here is the SC3K script file: https://drive.google.com/file/d/1bewSHZeiNxCYDvBHWstZWk253_BihybN/view?usp=sharing
and here is a MUGEN script file (Street Fighter II Turbo HD): https://drive.google.com/file/d/1am8kANoAurT0y39KvNpXbOAtsXPlmH6F/view?usp=sharing
As you can see, I have a lot of junk commented our as I experiment. (For instance, I can't seem to use xboxdrv to remap the controller for SC3K, even though the trick works for MUGEN games. Right now, I'm not even certain if xboxdrv is executing correctly as moving the "&" to it's own line causes a crash.)
Here also is a runcommand log file from the first attempt to play MUGEN after running SC3K - the one that fails until the second attempt: https://drive.google.com/file/d/1GlzoBk7S822F1H40kHe5W9Es08L9L0ca/view?usp=share_link
I know it's a bit of a mess. Let me know if I can clarify anything. Thanks for taking a look.