Settings live in user space. Software exist in containers like AppImage, Flatpak or Distrobox. If something need deep system integration, they can be layered on top of the system in the user layer. Immutable does NOT mean less control. Just exerting control over the system in a different, usually more systematic, automatic and deterministic way.
Ah yes, the immutable OS, except for all of the various mutable parts.
We should totally not call it anything less confusing.
It’s not confusing at all… How is this any more confusing than:
Flatpak - they’re not literally flat…
Snap - I’ve never seen or heard any evidence of something snapping by any definition of the word I’m aware of.
Dolphin - what the fuck is this, no sea life whatsoever!
Kate - this is a text editor, not a person.
Distrobox - not in an actual box.
etc.
The main difference to your examples is that an “immutable OS” is in fact mutable, while none of your examples describe themselves with an adjective that is contradicting with their function/inner workings.
Flatpak is a pretty good name, because it makes software flat in the sense that it avoids having a (tall) dependency tree.