I read the reference and the method to clear out all the edits is:
To get rid of tracked changes and comments, you need to accept or reject the changes and delete the comments. Here's how:
4. Do one of the following:
* In the Changes group, click Accept.
In the Changes group, click Reject.
5. Repeat steps 3 and 4 until all the tracked changes in the document have been accepted or rejected and all the comments have been deleted.
Notes
* If you know that you want to accept all the changes, click Accept, and then click Accept All Changes in Document.
so accepting the changes, which is what I've always done, does get rid of the embedded edits.
What is described in this document is hiding comments/edits through turning off some of the "Show Markup" settings. If you turn off the display of edits, then the document will appear clean but others will see the comments if they turn the Markups back on.
I've opened several documents where I recently "Accept all changes" or went through and accepted each one and I can't make the comments show up again. So I've never seen OP's behavior.
OP, is this repeatable? Open a document, make a bunch of edits, and save it. Then re-open it, Accept All Changes, use the Prepare/Inspect Document funtion on the Office Button menu. If it says there are no Revisions, Versions, and Annotations, save it and open again. If the edit marks are still there, then I think you have a bug.