Your mileage may vary, but because Word is the universal language of editors I’ve found it best to handle back-and-forth edits using Apple Pages (I gave up on Word some years ago). Pages handles marginal comments well enough, and does track changes well enough. Of course, if you have Word, it works just as well, maybe better.
When all the edits are completed and editorial is poised to transmit to production, I take that last edited copy as final (of course there’ll be one more proofing stage after the ARCs go out), open it in Pages (or Word), open the pertinent Project in Scrivener, create a fresh Folder called Final, then chapter by chapter, I bring it back in. I don’t need the granularity of scene-by-scene breakdowns. At this stage, they’re irrelevant. Copying back 28 chapters took me 20 minutes, tops, with arthritic fingers on the trackpad.
Now everything is back in Scrivener, and if any final minor changes are needed before press, I can just plug them into this Final draft. Sure, it’s not automated. But sometimes it seems as though we spend more time attempting to automatic every aspect of the writing life than we spend actually writing.