They do change daily but I'm not sure any one injury, even of an important player, can radically change them. (Safe to say that adding Stroman did more than our adding Vargas though).
Phillies rest of season schedule is considerably easier than the Mets, hence, my assumption that run differential is the biggest thing in this case (enough that the SOS gives the Phillies no advantage). I assume projected WAR up and down the roster factors in as well.