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. 
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