I don't know -- these are fair points.
I do know that when I was using GH regularly on a team where a number of people wrote clean history, the problems you mentioned didn't come up, not that I can recall. So for the 90% case, let's say, you can do clean history on GH and get the majority of its benefits. But yes, I'm sure it's flawed especially in workflows where those types of problem arise often.
Yeah that's probably fair. I haven't used a commit-centric workflow in a professional context, so I can't really say how often, if ever, these issues come up.