I think you're reading a lot more into it than is necessary. They are being overly cautious, having utterly failed to be cautious on Sunday. If the Phillies end up not having any cases this week, should they then not worry for the rest of the season about transmission between two teams? It's still a low risk situation - just not NO risk. And if the Marlins did infect even one Phillies player, then all of the Phillies would have been at risk playing again. The Yankees don't even enter into it by comparison, their risk would have been low. Though I also don't think it is caring more about the Yankees to treat the visitor's clubhouse as a hot zone for one day. And there's also the stadium personnel to think about (even if the Yankees planned to bring their own clubbies).
I never really understood how they were going to not have huge chunks of players out for 7-14 days until they clarified that the isolation was only required in the event of "close contact," but it seems to me that now applies to the entire Marlins roster, if not any Phillies (assuming there are no positive tests).
It also seems like it's not possible to ever truly be clear - the Phillies might all test negative today and yesterday and then have positives on Friday. If so, will that have been the incubation period from the Marlins or a new case that could have come from anywhere (players going home, travel to NY, contact in NY)?