I don't think we've ever been instructed on the minutia of where the spot of the pass is. I think in real time, I would just judge where the majority of his body is in relation to the goal line. Or maybe even the "center" of his body. If more of his body is breaking the plane of the end zone, then he's in the end zone. I'm just spit-balling. It kind of has to pass the eyeball test and I'd have to see it to rule one way or another.
More likely than not, we're going to rule this a safety. The QB is getting sacked, so he's getting shoved back into the end zone. It's going to "appear" that he's clearly in the end zone when he throws.
Obviously, if it's close, he's not in.