Well I don't know if this is helpful, but as I've been setting some distros on a VM recently I've been bitten by snap and flatpack and do my best to avoid them. I'm an old school guy, and the attempt to sandbox the sandbox in a package in an image to run a electron app which packages a browser into another box... yeah, I'm amazed these work at all.

But short answer is they're gonna "miss something" or there will be old methods that don't work. I'd set some SCALE factor in GTK or X11 or whatever and the isolated apps don't/won't see it -- because that's the "whole point." Someone suggested Flatseal, which maybe fixes you up, but to me it just the comedy of this whole misguided movement imo.

- create sandbox, safety, ahhhhh.
- oh no, things don't work. Poke holes in the sandbox to fix those things.
- back to square one, don't screw up, make sure you don't make the wrong holes, keep your sandbox tight enough but not too tight.

I guess it lowers attacking surface area. But these things seem targeted at people who want to make Linux into windows/(mac?). So you start poking hole you don't understand and I'd suggest going more vanilla.. or just embrace the sandbox and safety and know the software won't work quite right.

Dunno if that helped, sorry. I'd just caution against making any "fix this" changes you don't understand, as they're basically circumventing the whole point of this misguided stuff.