What I’ve seen is things like I ask a question about a piece of code during a PR, the author changes that code and my question vanishes into the ether with no indication (unless it’s lost in the noise of email notifications) that the code was changed and my question is no longer relevant (and if there was, perhaps an answer, the answer is also lost).

Yes. This specific aspect of GitHub is the reason why many teams don't want you to modify commits, but instead, add more commits. Which then also leads to squash-merging branches.

Other systems, like Gerrit, handle this much better!