Hi there, thanks for reporting these! I don't spend much time in front of my own computer anymore, and don't use this extension as much, so it takes me a while to notice changes on Spotify's front-end. I'll try to see if I can fix the buttons active status when I get the chance.

What "poping out" the window does, is creating a new window, then moving the tab to it. This sounds more like a bug on your other extension, as the tab shouldn't be considered as closed.
One thing to note, if you just resize the popup window large enough, you should be back to the normal interface.

The popup not remembering size and position on Linux is unfortunately a problem with Wayland, as far as I know. It can be remediated with KWin settings if using KDE, with mixed results. (You can also use that to make it stay always on top, which is neat)