It certainly does change that. He can't check in for the overwater leg until he gets to JFK. That's a very, very significant difference.
Why is that a "very, very significant difference?" If luggage needed to be claimed and rechecked then, yes, it would be a big difference, but that's not the case. What's the big deal about checking in? Am I missing something?
I would expect that business class check in, when luggage is already checked, would take approximately 2 minutes, maybe 5 if there is a line. Other than that, everything else would be identical to traveling on one PNR, right?