Karhedron, I don't see that Skywraith is saying anything that disagrees with you.
From the looks of it, it seems we all agree:
1. If it is an automatic wound that occurs in a different phase (such as from rolling a 6 to hit) Transhuman has no effect, as there is no wound roll.
2, If there is a roll that then generates mortal wounds on a given result (say, exploding vehicles, some psychic powers and stratagems), Transhuman has no effect as there is no wound roll.
3. If there is a wound roll where there would normally be an automatic wound on a given number (witchblades wounding on a 2+) Transhuman would prevent that wound if the roll is a 1-3, as it cancels out other rules that would apply to the wound roll that would otherwise make it wound.
tl:dr - if there is no roll to wound that occurs after the roll to hit, Transhuman can't trigger as there would be no to wound roll of 1-3 to trigger it. If there is a rules that would make a to wound roll pass on a 1-3 (whether from an automatic wound on a given wound roll, based on the comparison of S v T or from a bonus to the roll), Transhuman prevents that from occuring.