Desdichado
Hero
I never got that impression, and I've got nearly ten years now of experience to say that it's absolutely not true. I have seen this sentiment occasionally expressed by people on the internet, but it's a bizarre sentiment to me, completely disconnected from the reality that I know.3E gave the impression (whether true or false) of being a precisely orchestrated whole where you could only tinker with a few of the black boxes if you didn't want to risk system collapse.
You do recall the book Unearthed Arcana, right? The 3e version I mean?
I have no idea where anyone got the impression that it was "discouraged" or difficult to mess with any and all of the "black boxes" of 3e. Which really bore no resemblance to black boxes at all; they were rather easily reversed engineered, when the design principles behind them weren't specifically called out anyway so they didn't even need to be reverse engineered (monster building guildelines were in Dragon within a month or two release of 3e IIRC, and were officially included in the 3.5 MM. To use one example of the exact opposite of a black box.)