I ended up submitting a ticket for this and got the following reply:
I have received a reply from our devs and apparently, my guess was correct - the Start menu shortcut is needed for System notifications to work.
So, with this feature enabled, it is a planned behavior.
But they also advised that if you disable System notifications (Menu>Tools>Settings>General>Notifications) the shortcut technically might not be returned on the next run of the program.