Have your pop-up userform install a document variable in the ThisDocument.variables that contains both the update number and user choice. Then have your AutoExec in the Add-In check the status of those variables. This takes care of the "not until next update" one but not "never." Be sure to save ThisDocument after the checkbox is used and the variables are updated.

I am assuming that your Add-In gets written to the user's local computer's Word Startup folder when it changes.

On my ribbon Add-Ins, I use a dialog launcher to give an About dialog and make it optional rather than automatic.