Baseball is all about timing and routine. 5 days off makes a difference to these guys. Including the AL(one top seed loss so far), the top seeds are under 500. These are the top teams, so they should have a better than 500 records. 5 days off is disadvantage so far. The opponent may not be rested, but they have their routine and timing.
Byes are useful if you're burning through a lot of pitchers and need a reset for your staff, but they're a little scary if your team is in a rhythm. I think in this series the bigger issue was intensity/preparedness/confidence gap between the two teams.
The Mets were bottom 5 in the league on June 1st. So for the last 4 months they've been playing for their lives. Since getting 2 days off when Helene forced their Braves series to be rescheduled, they've played 12 games in the last 12 days, with all but one of them being essentially playoff games. They had to save their season with 9th inning comebacks twice since last Monday.
Meanwhile, the Phillies really didn't play meaningful, scary baseball games all year. They had essentially clinched a playoff spot, if not the division, before July was over. They then spent a few months twirling around, piecing together enough really ugly stretches to get some people worried and then countering with enough decent stretches to make the worriers question why they were worrying. But when it came down to it, one team was locked all the way in and the other was trying to figure it out on the fly. When the Phillies got punched in the mouth, their body language was "oh f*** oh no damn."