Making "Edit Collections manually..." work with Qt6 is actually surprisingly easy if you're comfortable with editing source code.
Just go to where your plugins live (~/Library/Preferences/calibre/plugins on my Mac), unzip "Kindle Collections.zip", and make a couple of minor changes to utilities.py:
where it references
QtGui.QTableWidgetItem.UserType
change that to
QtGui.QTableWidgetItem.ItemType.UserType
and where it references
Qt.ItemFlags
change that to
Qt.ItemFlag
zip "Kindle Collections.zip" back up, restart calibre, and it's just working for me. Hope this helps someone.