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Firefox PiP doesn't stay on top in GNOME
(feddit.de)
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Distributions include the Linux kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name GNU/Linux to emphasize the importance of GNU software, causing some controversy.
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This is a limitation of Wayland, aiui it's not currently possible for apps to set this by default. You can right click and select always on top for now.
So I am guessing that always on top works on the flatpak version because it is running through XWayland