You're right that "immutable" is a bit of a misnomer in that regard, and it's been argued that "atomic" is a more fitting term.

And I agree that a lot of documentation and how-to-guides don't account for immutable setups (yet?), which can get novice users especially in a lot of trouble.

Personally, I prefer a declarative system (NixOS) that solves this problem rather cleanly and gives me most benefits of so-called immutable distros as well.