Thanks for that
So I tried all of those things, but some of my settings ended up being slightly different. I couldn't package assets, for example. Eventually the game managed to launch, but I was stuck with a NW.JS screen. A bit more tinkering and the actual game launched, but then the gamepad controls were broken and nothing could be clicked / interacted with.
dop2000 suggested I try changing the way fullscreen was being called... and holy hell... that seems to have fixed it.
I must have spent days on this issue (literally). But it's working now. Just waiting for some other people to confirm before I get too excited, but this is the first time I've had it going on the Deck in a while (and without compatibility fixes).
Hopefully this thread helps others if they run into the same issue!
Thanks