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Great post - I figured that this would be the case based off of the idea that, whether you are male or female, certain markers can only be passed on through father/mother...
Your haplogroup, for instance, always comes from the father. It would seem to me, then, that things like haplogroups would only be linked to male genetics, and simply smushing together two men's genetics would result in things like repeat haplogroups and a total lack of mtDNA.
Perhaps, eventually, technology would exist that could translate the haplogroup of a female into the genetic code necessary for reproductive genetic combination, and likewise extract female-specific reproductive code from a male and do the same... But yeah, I imagine that would also just be the point of full genetic customization from top to bottom, and so the ability to do that would no longer be surprising but simply something that has come to us as a byproduct of advanced gene editing.