its only one document(name) in different versions?
So check in the document you get first from the supplier. Check it out, make your comments and check in again.
Now you have two versions, the original and the commented.
Check out the file again and overwrite it with the new file from the supplier and check it in.
You now have version three with the comments from the supplier.
We effectively do this when working with our User guides...
We create an empty PDF in EPDM from a Template so that we can assign a Part Number, description, etc. We have our User Guides created by an external company and whenever they send us an update we check out the pdf, overwrite it (copy / paste) and then check in and send it through the workflow for Revision control.