I honestly wouldn’t be too concerned about the space used by Flatpak dependencies
Space is a concern but not the concern, it's about download time. It's a considerable price of admission (worse with updates, though maybe not so anymore with legacy). I actually tried Flatpak at one point for Krita, and that is part of why I switched back to native.
You won’t get the most bleeding-edge performance features
EndeavourOS has been noticeably snappier
Yeah, I'm more worried about backtracking from my current setup (a bit more than half-a-year out-of-date but still newer kernel than Debian stable EDIT: correction). Particularly snappiness, I expect optimizations are a big part of that (CPU is Ryzen 2700, might be more important for that).