Interesting, that is good to know! I don't have any VR equipment (maybe one day!), however it sounds like the Flatpak has had some odd issues here and there that cause it to be a bit problematic.

I haven't confirmed it, but I think it has some issues with the controller I use (I'm one of those weird people who prefers the Google Stadia controller...), I was confused at when one day the rumble on it had stopped working, even though it previously worked perfectly (even after installing the steam-devices package). Later on I realized that I had switched to the Flatpak version of Steam to give it a try. I only say that I haven't confirmed it due to the fact that I had made plenty of changes to my system in the time between doing so and realizing what had happened, that perhaps something else I did affected it, but I have my doubts about that.

I personally prefer the native version when I can have it, one of the funniest reasons being that I like being able to see my currently playing music through MangoHud, which doesn't work in the Flatpak version of Steam (+ the Flatpak layer of MangoHud) due to the sandboxing (and I'm unsure of how to pinhole it through). It sounds silly, but its those small things that come up (but then also add up) as potential drawbacks between going with everything being sandboxed.