With regards to the links I posted - I know they're unbiased, I was just trying to get some info. I did try to find some studies from medical journals, but there are very few relevant ones :/ And for the ones that I did find, I was only allowed the read the excerpts. The Merck manual doesn't cite any of its sources, by any chance, do they? I checked out the doctor who reviewed that article, and couldn't find any studies by him that seemed relevant, though I'm still looking.
And I overheard something yesterday I thought might be worth mentioning. Two university kids were talking about having a hermaphrodite child. I'm well aware that intersex =/= hermaphroditism, but their respective attitudes were what struck me. The first kid said it would be 'cool', amongst other things, and the second kid responded with 'What? It would be a nightmare!' and went on to talk about how the child would have to go through therapy, face social rejection, and so on.
Going on the second kid's views, I guess stress might be one reason the parent-child bond would be affected? Sure, some people are understanding and handle it fine, but you'd undoubtedly get some parents who would be stressed and agitated from worrying about their child. They might subconsciously view the child as the cause of that stress, which would in turn colour their interactions with their child, and affect the bond.
Again, it's just an idea. I'm not trying to justify the manual's claim, just explain it.