Well, aside from the experiment, I would always assume that environment would be a factor. I think that's always been the case, since 1E days. Obviously, the severity of the environmental factors can vary greatly, but they're always going to matter. I mean, any combat that is purely a case of the PCs versus the monsters with no environmental factors is going to be pretty skewed toward the PCs. But even something as simple as distance of combatants is an environmental factor. Obviously that's one of the most basic factors....far less extreme than something like lava or other environmental dangers.
So again, outside the confines of the experiment/discussion, I think that almost anyone would expect some degree of customization by the DM, whether it's more environmentally based as Flamestrike's was, or more about boosting the monsters so that they present more of a challenge, as you described.
So, now taking that idea of assumed customization and then bringing it over to the experiment, I think it's just a simple matter of differing expectations. One party assumes everything to be as written, the other assumes that some design and customization is not only possible, but is necessary and, in fact, expected.
So I can understand why this was doomed to fail from your perspective...it was because your expectations and Flamestrike's differed from the jump. There was not going to be any common ground because of that fundamentally different view. I don't think that either party is wrong for that...it is what it is, and people play how they want and expect what they expect. So I think that anyone who expects DM customization would view any questioning of that customization as not trusting the DM...and that's what happened here.
But I do think that Flamestrike's view became clear as soon as he began posting encounters. I wouldn't say that his environmental additions were more dangerous than the monsters themselves in most cases. I think they added a level of complexity to the encounters that made them a lot less straightforward, and more challenging. To me, I feel he can clearly challenge a party of optimized PCs. And that was my expectation based on my own personal experience of doing that in my own game. Now, I don't adhere to the encounter guidelines presented in the DMG in any way, so I was curious about that aspect of the experiment.
But ultimately, I think we all assume some level of DM customization, even you by your own admission. Since that's the case, why even try to gage things "straight out of the box"? There won't ever be some universal version of the game that has no variances from table to table. The DM is always going to influence things.