What about the organic 70% of Shepard’s body? Are they also immune to trauma and heat that would dwarf an atomic blast?
Immune? No. Resistant? Obviously, yes. And while the initial tube-popping blast affected Shepard, there's no telling what happened after that. For instance, a biotic Shepard could lift a ME2-esque bubble to shield the damage from a safer vantage point, or some other damage-cushioning answer for the other classes. Clearly wasn't enough to kill, though I'm far from a fan of how they telegraphed this point.
And if she is fine, why does she look like an overdone road kill barbecue?
The armor in the breath scene actually looks no different than it did following Harbinger's blast and in the decision chamber.
Besides, didn’t the catalyst imply something about Shepard’s cybernetic bits could also be affected by the red beam? (or was that just in the vanilla ending?)
It did, and then Shepard took a breath of life. Oooooops.
Again I think I have to say this: the point I’m making is not that Shepard cannot survive, rather that can also be easily be assumed she can die in that ending, (regardless of that being what the player wants). And I'm sorry but the" Word of God" is by no means limitative regarding that point. It is just your interpretation of it that it is.
Do you honestly believe BioWare presented the breath scene,
the most difficult thing to obtain in the game, as a depiction of the last gasp before Shepard's death? But yeah, if you want to interpret it that way in the face of a structured Word of God and very obvious authorial intent, go for it.
I guess there's no real point in arguing over the details of the final sequence regarding Shepard's survival or death, because lots of things don't make sense in the series anyhow. Shepard's body should not have been salvageable after the Collector attack, yet it was. Anyone using just a flimsy breather mask in thin atmospheres should have pesky issues like blood vessels hemorrhaging in their eyeballs. Guess not.
The catalyst says a lot of stuff. Shepard's cybernetics? No biggie. Garrus, who is also augmented by cybernetics after the gunship battle on Omega, seems right as rain regardless.
Ding, ding, ding.