(Please add codebase project tags to tasks when possible, so such tasks can be found when looking for open tasks related to that codebase - thanks!)

Thanks for that @matmarex!

Checked this in the following ways:

1. For logged in users, user preferences are getting stored via mw.user.options.set and not for temp users.

Logged in users:

Temp users:

2. For logged in users, certain actions such as dismissing the education pop-up or the ve welcome dialog are getting stored via user preferences and both mw.user.options.get('visualeditor-hideusered') and mw.user.options.get('visualeditor-hidebetawelcome') returns 1.

For temp users, it's getting stored correctly in Local storage in the ve-hideusered and ve-beta-welcome-dialog entry instead.
User Ed pop-up: