It was a little surprising to me, given how key rebases are to the stacks workflow, that rebases are not handled very well in the Graphite UI.
I like how
https://reviewable.io/ handles rebases. The "file matrix tool" allows you to see the state of the PR, including diffs and comments at any point along the timeline of rebases. It shows which revisions have been replaced by rebases, and allows you to select any subset of them to review. It also shows which revisions have actually been reviewed as a reference.
Comments will show inline on rebased code, when it is possible for the system to guess what the comment applies to, with annotations like "Probably rebased from xyz", otherwise they show (IIRC) as orphaned comments.
Here is a screenshot from a review I had lying around with a few annotations:
The interface is definitely more complex, but once learned it is very powerful. As things stand right now I'd still use it over Graphite for the actual review process.