Hidden apps have always been installed. Just Hidden. Or Restricted in Apple Parlance
The reasons that they are not uninstalled is:
1. The app doesn't lose any data when hidden vs being uninstalled
2. If you unrestrict the app, it appears instantly, instead of having to be installed again
Regarding the side loaded vs App Store for system apps.... That's a new one. I'd, for visibility and sanity, open a case to seek clarification.