Here’s a real-life example from me that demonstrates why I consider it crucial to not flatten PDFs on export.
I was reading some PDF materials the other day and need to reference another book I finished ~5 years ago. I searched for the book and found it in DEVONthink, but soon realized a large portion of my annotations hold little value to me now due to my limited understanding of the material when reading it for the first time. But because I made those annotations in GoodReader, a robust PDF reader I once relied on which did not flatten my annotations, editing those annotations 5 years later is a trivial task.
All the tools at the core of my workflow do not use a proprietary file format. In the case of PDFs, I can create / edit / delete annotations in DEVONthink or PDF Expert knowing my works are future-proof, i.e. future me will be able to edit them when, not if, he disagrees with present me.
MarginNote offers a unique workflow not easily replicated otherwise. But until I can export my data in a non-destructive way, I have no other choice but to regretfully avoid it.