Good article by Neyer. I'm not sure why you found it "surprising".
When Bill James first started writing abstracts back in '80s I became an instant convert. Over the years sabermetrics has ballooned. Now...it seems that sabermetrics is the end all...each new development taken as gospel. Not at all what James planned.
Like most prophets, he wouldn't recognize a modern religion.
The "gospel" component are the outsiders--websites, bloggers, posters, etc. Way too much rigidity.
The insiders--the younger, cutting edge, educated folks who grew up reading James and others--are a different sort. They tend to actually interact with a more diverse population and most are inherently skeptical of dogma and are comfortable changing on the fly when circumstances warrant. Cubs leadership know all the sabernetric stuff too but hard to listen to them and conclude anything is gospel to them.
Think all of this is useful, even the dogma. Just have to separate the wheat from the chaff. This has been true of every advance in every discipline, ever. Skepticism is the foundation of the James Abstracts too. Skepticism permeates almost every page. The New Dogma warrants skepticism too. No different than anything else.