I have fixed the Issue, it seems it was a problem with the .desktop file located in
/var/lib/flatpak/app/org.strawberrymusicplayer.strawberry/x86_64/stable/fe501a8f671451ccb6eeb6f26f144b25c43ee460b69b92d4d3895ceb7337adcc/export/share/applications/org.strawberrymusicplayer.strawberry.desktop
All I had to do was replace the Exec line with Exec=flatpak run org.strawberrymusicplayer.strawberry
No idea if changing it from the default will have any negative effects, but I now have Album Art in the media controls when launched from the Application overview in Gnome.