I hadn't even thought of this. We had a similar discussion a while ago over what happened if embarked units took damage from the admech reflection ability.
From what I remember, we reached the consensus of either; Nothing happens, the mortal wound vanishes into the aether. Or, from a more fluffy perspective- the vehicle takes it.
That said, I still disagree with the fluffier idea of the vehicle taking it. From a rules point of view, it would make sense for nothing to happen, and the mortal wound to simply vanish.
EDIT: Looked over the admech errata: Apparently the unit that is embarked takes the mortal wound from the invulnerable save. So, yeah, if you use dark technomancers from inside the transport, that unit can have models die.
~Kabal of the Black Dawn
~Coven of the Dark Heaven
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