It has an option to toggle auto resume (Alt+r ) this change is saved and seems to do what you want. I was not sure if the third tab behaviour should be kept, I now think that it should only resume one prioritized by the order of last played.
If you have suggestions for how it should be implemented, https://github.com/NDevTK/AutoPause/issues/7

Update: changes have been made in version 2.3