Atomic in software refers to an operation that cant be interrupted because it happens in one step. This one of the big selling points of atomic or immutable distros. Your system will not be left in a broken state by cancelling an update because updates do not take multiple steps, unlike traditional distros.

It means a change either applied completely and successfully, or not at all (think “atomic transactions” in databases).

How could you install anything or change any setting if it was truly immutable?

Immutable OS makes sense in certain scenarios, but not in home computing.