This is most certainly an issue – though I’m not sure it’s as terrible as people might imagine. I’d like to propose an option along the lines of Option 2 (which I find highly interesting). Perhaps it could become policy that contributions be merged as a squashed commit for non-vendored code alongside a second commit which includes additions/modifications to the vendored code.
I’ve updated the repo above to reflect what that might look like. Regardless of the outcome, I’m curious to see thoughts on this matter.