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Pipewire vs PulseAudio: What's the Difference?
(itsfoss.com)
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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).