Manual save-points are still useful though if you want to go back to a previous version and branch off a different experiment.

Pretty much the same how (mostly PC-) games combine auto-save, manual quick-save and manual 'explicit' save (with a name chosen by the user), and where the last N auto- and quick-saves are preserved (where N is usually a fairly small number). It's less about not losing progress (for that, having only auto-save is fine), but being able to go back to a previous 'checkpoint' and branching off a new timeline.

Agreed, I'm seeing people of all ages not having to interact with the desktop metaphor at all any more. Typically people that manage to do all their "computing" on Android, iOS or sometimes ChromeOS (where they are email and SaaS based).

The metaphor is more of containers/projects and save slots/objects. Far more like video games than the traditional model.