In a back-handed, way, I think we are agreeing with each other. We are both arguing that the scenes in question add to the development of the character and their growth. One deleted, one kept.
The Tony/Pepper scenes, as you say, add to Tony's arc at the end of the movie. I am saying the same Steve's scenes. Although, there is certainly more mass-audience interest in Tony/Pepper than in Steve/Waitress.