I think Altas's concern here isn't that he's chasing her, but that all this time together isn't productive in terms of what she needs. She seems to need space, but having Atlas around all the time isn't meeting that need. I could be wrong here, but that is my interpretation of his concern.
Altas, if there is a way for you to see your son on those days too without your W being around, maybe consider that. Or, if you think it wouldn't hurt (and actually help because it shows you're trying to give her time and space), bring up this concern about smothering to your W and see what she says. Yes, it's R talk, but I think it may be appropriate in this circumstance.
