Returning from steam overlay some GUI actions are not possible

I didn't check all of them, but some examples are:

1. buttons on the main menu,
2. buttons in any building or vehicle menu - like changing the name of the vehicle depot is possible but other buttons or slides don't respond to mouse click,

when you alt-tab to another OS window and back it works just as before,

I do suspect it's a Linux+Proton issue so here are my specs:

Kernel: Linux 7.0.10-2-cachyos
CPU: 12th Gen Intel(R) Core(TM) i5-12400F (12) @ 5.60 GHz
GPU: NVIDIA GeForce RTX 3060 Lite Hash Rate [Discrete]
NV Driver: NVIDIA-SMI 610.43.02
Display (C27F390): 1920x1080 in 27", 60 Hz [External]
DE: KDE Plasma 6.6.5
WM: KWin (Wayland)
Cursor: breeze (24px)

I hope this is enough to allow the dev to diagnose this and resolve

I have experienced a similar issue, but ordering the key board combination to toggle the steam overlay even when it isn't visible fixed it fit me

I don't understand what you mean - can you point to where this is done ?

Well for me, also on Linux using i3wm, I have to enable the steam overlay in order to be able to switch to a different workspace. (I consider this an issue of i3)

So:

1. hit ctrl-tab to enable steam overlay
2. hit ctrl-mod-<other workspace #>
3. switch back to CoI. Game appears without steam overlay, but all the same issues if buttons not working
4. hit ctrl-tab to enable steam overlay (perhaps again to remove it) this fixes the issue

for me the fix is ALT-TAB to another window and back to the game fixes the issue, but it's not the way this should work. then again, if it's only on linux, than no one would care until it hits the Steam Machine or steam deck and those players will start to complain