I've been searching for this since the day the game released.
The game always minimizes itself when I switch focus to a different app in borderless and fullscreen modes.
The only way I've been able to get it to not minimize on focus loss is if I choose windowed mode. This is not ideal for me because I would still like the window to at least be able to be maximized. But windowed mode restricts me to a few specific resolutions. None of these resolutions properly fit the screen. The l
I was having the same issue and someone on the Discord pointed me to a utility called. "Borderless Gaming" You can purchase on Steam or D/L free from GitHub. https://github.com/Codeusa/Borderless-Gaming
I run dual monitors and this utility scales windowed mode to full screen borderless. I'm now able to mouse back and forth between monitors without KSP2 minimizing. Not sure if this will help on Linux but there is a source tar.gz on the GitHub so you can try compiling.