There's an extension for that afaik
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I usually right click the window in the app bar and choose the "stay on top" option. This issue only happens in Wayland, also. in X11 it stays on top as expected.
does anyone know if there is any work on like a portal/wayland extension or something to enable the ability for applications to get permission to create an always on top window on wayland.
Yes normally Wayland surfaces can be displayed at the top. The plasma Panel for example is always on top
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