This is a project to manage Blender's application templates.
Mon, Aug 14
@Campbell Barton (campbellbarton), mind having a look here?
Wed, Aug 9
Thank you for the explanation Campbell,
The logic is - many preferences are things you wont want app templates changing.
Tue, Aug 8
Oh, you're right Campbell, I overlooked that part. Still, it doesn't make any sense to me why only keymaps, addons, default startup,themes... should be allowed and not whatever setting in user preferences. Yes, users can still control any of user settings(eg. in Interface tab) via API, but the same way users can control via Api, those(keymaps, addons...except splashscreen), which are now allowed via app. templates.
This is working as intended: see https://docs.blender.org/manual/en/dev/advanced/app_templates.html#detailse