Why does this happen? On the left, a screengrab from a marked-up PDF, on the right the result of the comment import into InDesign.
What happens if you allow the auto-edit to populate in? Does it show up in the right place?
I'll try to run some tests next time I see it, but in general, as a workflow step, that wouldn't be an option for me. I have to worry about reflow and the PDF markup is not reliably consistent.