As for the auto-add file type issues, Calibre doesn't seem to offer a plugin API to extend the book file type extension list, but I just found a hack / workaround that allows my plugin to tell Calibre to consider ACSM a book. Not sure how reliable this will work with future Calibre versions since it's not a stable API, but it's better than nothing.
This will both fix the issue in the "Add File" dialog (having to select a different filter) and will also mean that the "Allow any file type" auto-add setting is no longer needed. This fix will be included in the next plugin update.
As for the metadata issue, I just tested that as well and had the same thing happen, but there's not much I can do about that from within my plugin. I can't see anything unusual in the logs of my plugin, so I have just opened
a Calibre bug report for this. The bug has been fixed now, so the next release of Calibre (5.29) should work properly with auto-adding.
EDIT: v0.0.8 is now available which fixes the Add File dialog, and no longer requires the "Add all file types" auto-add setting. The metadata issue is still present, though, that will need to be fixed in Calibre.