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Untested because I can't be arsed to build this thing. The problem is that the MPRIS bus for an app should be org.mpris.MediaPlayer2.$APPID so in this case org.mpris.MediaPlayer2.org.js.nuclear.Nuclear but it is org.mpris.MediaPlayer2.Nuclear_Music_Player. Flatpak enforces the bus naming so it doesn't show up outside the sandbox.
As a workaround one can override the flatpak permissions so that nuclear can own the bus name org.mpris.MediaPlayer2.Nuclear_Music_Player on the session bus.