Sorry about that - I was about to answer it but a stray cosmic particle just happened to knock the thought into oblivion.
As far as Registry settings go, yes, those would be the only keys. (Although you might as well just go up one level to HKxx\Software\MicroSabio, which would pick up an stray A-Shell settings that aren't specific to ATE, such as private XTREE configurations.)
Note that all the settings associated with the Settings and File>Save menus are stored in files though. Ultimately, they could be anywhere (if the user takes full advantage of the Save As option, and adds a command line switch to point to the saved settings in some odd directory), but mostly they would just be in the places identified on the File>Save dialog.