I remember a lot of people kicking up a fuss about it years ago saying it’s a mess
I remember the same type of discussion when PulseAudio was new, nearly 20 years ago. It’s just growing pains. I hopped on board with PulseAudio ASAP back then, and yeah, it was kind of a mess but it did what I needed, and the alternatives did not.
I don’t recall having any audio issues in recent years, either on PulseAudio OR PipeWire. But then again, I’m still not running Wayland (I plan to…soon™) and this is the first I’ve heard of issues with Flatpak (maybe I’ve been using PipeWire longer than I’ve been using Flatpak; can’t recall).