I'm afraid not. Because since you can edit in the diff output window, if you insert lines on one side, Imaginary Buffer Lines will be added to the other side. Same if you delete lines on one side or another. This would be difficult to track.
The right way to do this is to copy the buffer, diff that, and then overlay the results of that on top of the actual buffer. So that you can undo the everything that happened in the diff as one undo step. It sounds very straight forward. However, DIFFzilla has a lot of capabilities beyond "normal use" that affect this (diffing line ranges, diffing specific functions, source diff, etc) it complicates things. Plus, as I said, the diff has been in the editor for twenty-one years. So to do it right, some things should/would be cleaned up at the same time.