I tried to add the option to show AutoPlaylists in the panel, but since the AutoPlaylists are basically internal queries, I cannot query the PlaylistSongs table to find out whether a given track is on an AutoPlaylist. In other words, I can show the AutoPlaylists, but I can't find out whether they should be checked. Sorry.
The way I see it, I'd have to parse the search conditions stored in the AutoPlaylists and execute one query for each AutoPlaylist every time you click on a track in the track browser. Not fun for either of us.
In other news, I updated the script again, fixing a bug that might screw up the settings for the LyricsViewer plugin, if you have that installed.