My best guess :

>! A schizophrenic man had a sex change and married his adopted brother. The "marriage" is a genuine marriage, but is between a man, a (newly-made) woman with the same parents but no blood relation, and the male alter-ago of the transexual. No clue about the chromosome part, maybe part of the surgery involved cutting one off.

Just in case this is somehow not the correct answer (though I wrote this before reading the 3rd hint...),

>! I *do* think two of the 'men' are the same person, somehow. I think in fact 46 of their chromosomes are identical and the 45 reference is a red herring. If they're identical to the *atomic level* surely it's impossible for them to be two different people?

Also,

>! Pretty sure sex change is involved somehow. The question even says at marriage they *were* men, which is ambiguous as to *when* they were men.