Matt,
Specifically, I have toured many Philly, NJ, NY, CT, MA and Long Island and and played some. There is a clearly higher number of courses designed by top gca's in those areas that are in the top tier of the world. Texas may have none of those.
While I have basically concurred with your opinion, I see a lot of the courses in Philly, like Philly CC, Lehigh or Hungington Valley as both in about the same league as Colonial. I grant Colonial is flatter, but in architectural features, it's not inferior to most NE Golden Age courses.
You talk about Dan Jenkins being a Colonial supporter, which is true. But down here, and elsewhere, we all reel from the NE centeredness of all media, which gives anything worth supporting in the NE a huge advantage over other areas of the country, including golf course rankings.
Colonial, because it hosts a national tourney, is caught in that restoration vs. modernization question more than most. If they choose to keep it substantially the same, Colonial scores will go lower. But, is that necessary when its a great members course, and substantially the same challenge it has always been?