You’re treating a commit as an atom, which is not true in patch based git situations like Linux.

Most of the rest of us do not work this way, but they still do. The rest of us also only have to deal with three way merges most of the time, instead of octopus merges. Though I jokingly call, “fixing an incorrect three way merge” a “five way merge” because you end up doing a star shaped pattern of diffs to re-resolve the code to retain the intents of all three versions. A to merge, B to merge, merge to HEAD~, A to HEAD~ and B to HEAD~

I'm not really sure what you mean by this. Git treats commits as atomic (unchangeable), and thus they are atoms (indivisible). This is not really related to patches, unless you're referring to partially applying patch series. Can you elaborate on what you mean?