After I choose new resolution and deselect full screen option, the program shows a preview, but I can't click "yes" to make those settings permanent. The count down continues and the program switches back to full screen.

Same thing here.

Can you try to task switch out of the app and switch back in? This should fix the issue that you cannot "click" into the game on some Linux distributions.

Thanks for the reply Catmic, however it didn't work for me (Solus).

Can you try to start the game with "-screen-fullscreen 0" and see, if that works? 

Which version of Solus are you using?

Thanks, I can confirm running `RotT.x86_64 -screen-fullscreen 0` from terminal launches the game in windowed mode, and then the resolution can be changed in game settings. I could perhaps make a script to do that, since I didn't see a way to launch with options from itch.io itself. Maybe I can with Lutris though.

Solus is a rolling distribution, I'm up to date, using the Budgie flavor.