Seems to me that the story sets Shep up for that last scene, no matter the choice, Shep is either blown up, toasted by electricity/energy,transmutated and diseminated through out space or harvested.. None seems so good for Physical Shep. So I assumed he/she never made to the catalyst lair, but instead was just on the ground all hidden and buried in rubble from that wicked reaper blast. Mostly because there is never the correct garb worn,and it's probable that the beam it's self was designed to pick up 'dead' stuff for harvest.
That way, when up there farting around, Shep is just a reflection of his/her self. The choices are all from the crucible and the citadel, the data from those decisions is all that's needed from Shep. Shep is still on the ground the whole time. Mortally or not, wounded but communicating with the catalyst, as the story puts him/her working up to that from every incident regarding the reapers and the idea of ending the cycle. All the mental pictures and weird dreams and the cypher and Asari Shep communed with. All point to extra sensory perception for communicating. Its not speculation to figure Shep does this, and explains, kind of why the reaper that shot at Shep, went on about other business just after.
The breath scene doesn't really make sense,even if with the necessary game stats, to get a living breathing Shep, IF the game builders were in the mind of ending the Trilogy. It's no way to end a hero rant, with the hero not at least riding off into the sunset. With that breath, we're stuck with either Sheps OK, or Shep made one last hurrah.
The strangest part of it that this scene only occurs with 'destroy' and no other? That would infer that destroy is canon, as saving Shep is paramount for ALL players... At least one person from the devs side, infers that it 'could be' a last breath. But many dis that as disinformation, or generalization of some sort. This all is too much head canoning and unessissary metagaming to understand if or if not Shep lives. The game seems to point that Shep does not, other than that breath scene, where it is only ONE breath, not enough to say it's over,just enough to say it isn't.
Who ever thought that one up had a bad idea, unless they wanted players to get upset over it for some reason, OR they intended to leave an opening for a possible comeback for Shep. I didn't like the idea of the scene with the supposed LI getting all hopeful and having some 'realization' either.. A little too much fiction there as well. It would've been easier to just plan another game or something. imho