> Had you simply rebased you would have lost the ability to separate the initial working implementation of D from the modifications required to reconcile it with M

I'd say: cleaning that up is an advantage. Why keep that around? It wouldn't be necessary if there was no update on the main branch in the meantime. With rebase you just pretend you started working after that update on main.

For the reason I stated that you quoted right there. Separating the potentially quite large set of changes of the initial (properly working) feature from the (hopefully not too large) set of changes reconciling that feature with the other (apparently incompatible in this example) feature. It provides yet another option for filtering the irrelevant from the relevant thus could prove quite useful at times.

Recall that the entire premise is that there's a bug (the allergy). So at some point a while back something went wrong and the developer didn't notice. Our goal is to pick up the pieces in this not-so-ideal situation.

What's the advantage of "cleaning up" here? Why pretend anything? In this context there shouldn't be a noticeable downside to having a few extra kilobytes of data hanging around. If you feel compelled to "clean up" in this scenario I'd argue that's a sign you should be refactoring your tools to be more ergonomic.

It might be worthwhile to consider the question, why have history in the first place? Why not periodically GC anything other than the N most recent commits behind the head of each branch and tag?