Not an answer, but "MCID n already present" -error appears in PAC (and in axesPDF which contains PAC) as soon as one edits the existing content in a tagged PDF so that some object is somehow rebuilt. Seemingly the tagging is something extra on the basic PDF structure and PDF editing handles tags only with the left hand.
An useful thing to do is to open Acrobat's Content panel which shows the objects, their layering order and tag containers where the objects are placed to.
PAC "MCID n already present" -errors stopped to appear after my PDF edits when I moved possibly soon to be affected objects out of the tag containers in the Content panel and deleted those containers. Then I did my edits, typically moved or changed some text and retagged it.
A person who really knows what Acrobat will do when one make edits maybe could tell which objects could stay in the tag container and move out only those which will be affected by the edits. And then move them back after editing. Moving all content out of the tag container and deleting the empty container, editing and finally retagging in the usual way after the edits has anyway worked.