For a while now the upgrade tasks are among the most popular and the windows with Model store has been changed is a part of the process. Last week I worked on one upgrade from AX 2012 R0 to R2 (so it was an in-place upgrade), and at the end of the process after completing the Data upgrade checklist for in-place upgrade the window kept appearing although all the items in the checklist have been Marked as completed.
After trying everything I knew of, live running the Prevent checklist, setting the noInstallMode on the model store, etc, somebody came in and opened up the Data upgrade checklist and checked a bunch of other steps as Marked as complete, as well as selected the well known Disable the Upgrade checklist. Well, even though we were performing another type of upgrade, doing this seems to have done the trick and the window stopped poping up. Excellent.