You could just name the MIDI Config Simple, Clean, Minimal or whatever. You don't have to have User in the name, but it should work even if you have.
The MIDI config is global. The settings is'nt preset based. So saving the sound preset like you say you do, have no impact on the MIDI Config. Just save the MIDI Config. You don't have to save the sound preset.
(I can also recommend you Export your MIDI Configs, and then create backups on your files, so you don't loose the configs and have to create them again.)
The saved MIDI Config should be found in the same section afterwards.
I don't have an Arturia controller, but i don't think it matter.
The MIDI Controller and MIDI Config settings in Stage 73 V2s sidepanels MIDI section, that you have, when you close the application, should also be the settings that is present, the next time you open the application.
So if you in example change the MIDI Controller and MIDI Config settings and close the application, then you will not get the previous settings back just by selecting the sound preset you say you also save, as the settings - as i said - is global.
If the above is'nt the case, then try to clean the Stage 73 v2s Prefs through ASC.
If you afterall have any MIDI Configs of your own, then export them first. Then they allways can be imported again.
BTW. You don't have to be in MIDI Learn mode to remove an assigment. Just right click over the parameter in the sidepanel, that you wish to delete. A pop up menu give you some options. Also to delete the parameter assigment.