I am unable to reproduce the bug. Ctrl+A does not toggle 'Always on top' when the Playlist or Media Library is in focus. Tested with classic and modern skins.
From the Shortcut key list (via the 'Keyboard shortcuts' tab in the About Box)
Ctrl+A Toggle Always on Top (N/A in playlist editor and media library)
Ctrl+Alt+A Toggle always on top (playlist editor)
Knacker got there before me. Good Job