I noticed more-or-less by accident that subfolders in the User Commands have a "Sort contents" option in their context menu that allows the commands in that folder to be sorted alphabetically (and by extension I found that Show Folders is also supported for Global Tables, User Events, and basically all the other options!)
I would be very happy to see that option extended to the "main" Toolbox item, so that I can right-click "User Commands" or "Global Tables" and just sort everything without putting it into a folder first.
Conversely, an option like "Add User Command" turns out to only be on the top level. It would be great if that option would also be available on the folders (and would create the command directly in the folder).