The value the Phillies get out of having consistent, geographically friendly affiliates is more important than anything else I'd think (and I mean the baseball value not the marketing value, though that obviously counts too). The Mets just moved their AAA team from Las Vegas to Buffalo. The Nats are moving theirs from Buffalo to Fresno as a result. The Rangers just lost their Texas AAA team (which used to be the Astros, and was also the Astros' AA team, and now is the Astros again) and are heading to Nashville. Controlling park factors, let alone having them the same at every level, would be a huge luxury.
And they still play half their games on the road. It's up to the baseball operations staff and coaches to manage these things (and factor them in) and have a consistent approach throughout the season, home and road. Ultimately the players who didn't make it probably weren't going to make it regardless. Seems to me a lot of the "Reading wonders" still did pretty well at AAA too. They just weren't big-leaguers.