So, because of using scancodes, remapping keys in your OS doesn't have any effect on the game. This is intended.

Please, please reconsider this, even if only on Linux.

All of the listed "issues to solve" at the bottom of the post by @posila would be fixed by letting the user's OS-level key ...

I have the same issue. I normally have caps lock and control swapped in the same manner as others in the thread. I also use a dvorak layout - this means that where most people use "wasd", I use ",aoe" - and this seems to be working fine. But when ctrl:swapcaps is set, the game never detects that ...