Reading some comments on other forums, there is speculation that the 2 Howards switched again. Pointing to how Howard Prime mentioned to Baldwin he made a "new deal" and how Howard looked during the crossing. That perhaps he gave his other a chance to reunite with Emily Prime and really connect with his daughter. I didn't consider that when watching the finale and took it as Howard Prime realizing he should go back to his world and should have left a long time ago. I can see either version