This is purely a probability thing. We’re overthinking it.
The Phillies were a slight favorite to win the series, but let’s say they were a coin flip to make it as overwhelmingly fair as possible. So they’re 50-50 to go through the Mets series. Play it out 100 times, they get to the NLCS 50 times.
Let’s say the Phillies would have been a 55% favorite to win a 3 Game WC series, which probably isn’t even true. That means 45% of their outcomes are chopped off immediately. We now have a max NLCS outcomes at 55/100. Now let’s apply a 55% chance to win the NLDS because you believe they should no longer be at a disadvantage. 55% of of those 55 outcomes where they won the WC round leaves us with 30.25 out of 100 playoff runs where they advance to the NLCS.
50 vs 30.25% is a cataclysmic difference. That even assumes this proposed disadvantage doesn’t dissipate after 1 or 2 Games. Every number here was overly kind. No matter what you do, you cannot get a disadvantage in the following series to outweigh having to play one less. Byes are the best thing you can possibly get in all situations.