Are you using Wayland or X11? (find out by entering "echo $XDG_SESSION_TYPE" into a terminal)
I suspect you're on Wayland, because that's what I'm using and I also can't click anything when using a non-native resolution. I used to be able to get around this by editing the executable but as you can see that's been broken since October. For all the good Valve have done for Linux gaming, they sure don't seem too bothered by their flagship being busted.
This is where I've just given up and switched to native res (as I want to keep using Wayland) but you might be able to make it work by switching to an X11 session. What distribution are you running?