DKR began as a What-If tale, it only became part of the DC Multiverse after that was brought back in Infinite Crisis. Even so, it being on a different Earth, it depicts a different Batman and Superman who are wholly separate individuals from those featured in the regular books, and can be considered outside the continuity of Earth-1 being it's an entirely different continuity on an entirely different Earth. Argue semantics and miss the point all you want, it doesn't change those facts.
And say what you will about us being privy to their thoughts doesn't mean anything. I person can be in denial to themselves, after all. And yes, Batman and Superman have both come a very long way from their origins, but 70 years will do that. While they had to be changed to even consider a friendship with each other, those changes have taken place and taken root. If you'll recall, the same changes had to make Batman not look so, you guessed it, homosexual!
And I don't actually believe that homosexuals are born that way, that's just an excuse closet homophobes use to make them feel okay with it. The deal is to realize that nothing's wrong with being gay whether it's biological or not.