Perhaps xboxdrv could help?
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I use highly customizable tiling manager, so I more or less automated these things where I switch bindings depending on what window is focussed. I think though that if you know how to rebind the mouse click manually you can just automate it through bash script.
Basically First line, rebind everything Second line launch the game Third line, rebind things back.
I am using steam (yeah, I'm sorry)
I guess I could pgrep the games process and if it isn't present then kill the xbindkeys.
Maybe you can do something like that in the launch options:
xbindkeys <stuff> && %command% && pskill xbindkeys
I don't remember the game run command but it should be similar to %command%
or something...