Sony's developer rules are like YouTube's content policy: arbitrarily restrictive, but may be waived for favored parties. For example, SCEA (but not SCEJ!) had a "no sprite games" rule. The American marketing for the PlayStation leaned heavily on its 3D graphics and overall "next-gen-ness". Games that relied heavily on 2D sprite graphics were seen as detrimental to the console's image because they looked like something from the fourth console generation. But big-name developers could get exceptions for flagship titles, as Capcom did for Street Fighter Alpha and Mega Man 8. So we lost out on interesting sprite games from smaller developers that were released in the Japanese market because of this policy.
It's no surprise, therefore, that Naughty Dog got away with violating a Sony policy -- even about messing with system memory -- to create a "system seller" title.
Yes, the article in reference mentioned other developers harboring conspiracies like ' secret PlayStation libraries' supposedly at naughty dog's disposal, but actual credit by the developers was to their use of Lisp as a secret low level language, though admitting they also bent\broke some rules in the process.
It's no surprise, therefore, that Naughty Dog got away with violating a Sony policy -- even about messing with system memory -- to create a "system seller" title.