The Nats' expected W-L record on July 30 was 57-48. After they beat the Mets 25-4 it was 59-47. That same day, the Phillies' XW-L went from 55-51 to 56-51 because they beat the Red Sox 3-1.
So the blowout was only worth one extra win for the Nats. I tend to think all of these things even out. There are also plenty of other factors (mostly luck, as represented by one-run wins, above-average bullpen performance) that explain deviations. And yes the formula doesn't really account for injuries or personnel changes.
The Nats also lead the division in runs allowed, albeit not by much. But that's probably a bigger factor in their differential than the occasional blowout.
And the Braves are actually the team with the best Pythagorean in the division, and have been all year I think. The Nats just have the bigger deviation.