After a fair bit of trial and error, just wondering if anyone has any further pointers - could a fullscreen window (rather than just fullscreen) potentially work for this? I'm envisaging the full screen being the size of the widescreen, with the window being 4:3 - potentially the emulator would still register the hit outside of the displayed screen. I'm struggling with the Retroarch GUI options for this though.

if what retrowertz suggested doesn't solve your problem try to set mouse index to '0' for every user binds

Hi
I wanted to know if the lightgun is compatible with LR-FBNeo
is it possible to have a list of emulators compatible with it present in Retropie? thanks

Hope it helps someone! I tried to get the mouse to work as a Zapper. It just wouldn't work. End of the story: I had to unplug the USB-dongle of my remote control, because it had a mouse functionality. I think it had a conflict with my wireless USB mouse. Afterwards I changed mouse index to 0 in lr-fsceumm under Controller 2 Input and changed the type to Zapper. That's it!