Is it safe to manually delete Backup folders?

I have Scrivener set to keep all backups, as I want to manage which backups get deleted and when. I assume it’s safe to manually go into the backups folder location and just delete whichever “project.bakx.scriv” folders I don’t want, but I thought I’d better check and confirm that before actually doing it. Is this a safe way to manually manage the backups that are retained on my computer?

Yes, that’s perfectly safe to do. If you have the rotation feature entirely disabled, it won’t try to do anything with existing project backups and will just keep adding new ones, blindly.