When I hear people saying "Why did Mt. Everest form?", I can substitute "How did..." in my head, but it also makes me wonder why they used "why" in the first place. No biggie, but that's only because we know a fair bit about geology and how mountains form.

To me it seems a proper use of 'why'. It means: consider the world as it was at some time in the past before Everest existed. Had we been alive then, we could imagine a future where Everest would form, or a future where it (counterfactually) would not form. The correct prediction would have been to say that it would form; we know that in our own present. But of a person reasoning only from what existed in the past, we can ask, why do you predict that Everest will form?

That is, to me, the meaning of the world "why" used about objects: it asks why the past evolved into our present rather than into a counterfactually different one.