Well said. I basically agree with that. Marvel sales haven't really suffered for having several Spidermen and such, have they? I don't follow Marvel that closely, but I know they have at least Peter Parker and Miles Morales as Spidermen, don't they? And it seems to keep everyone happy- everybody gets the book they want with the character they want, and then some of them decide to buy all the different variations on the character just because versioning isn't as important to them or they like both guys. It's a formula that seems to work.
I also think comic book buyers are sophisticated enough to "get it" that there are two Supermen in two different universes, or that there are two Clark Kents in the same universe who are different people with different roles. We've moved from comics being read mostly by kids to mostly being read by adult comic book geeks. The adult comic book geeks know this stuff about alternate universes and different iterations of characters better than the writers and editors themselves in some cases.
It's not a problem.
Like you said, I do think you make an effort to differentiate- like one Superman has a beard, different costumes, etc.. I mean, new52 Superman already has that sort of built with the high collar and the body armor (Which I think was gone by the end, but they could bring it back) and the red boots and whatever versus SuperDad's more traditional costume plus blue boots. They could accent those differences even more if they wanted to- even all the way to Superman Red and Superman Blue style (Without the body modifications- just the suits). They could also feel freer to accent the personality differences more heavily, and even more clearly show SuperDad's wrinkles or have him go gray, and revise the younger Superman's age to like 25 or whatever (Not saying that part would be what I want, I'm just saying they could, if they were worried about the characters being too much alike). They could also do story tone differences, make SuperDad more PG and new52 more R-rated, etc.. Different art styles in the books. So many different ways you can do this.
If they really had to, they could even make one of these guys not Superman, but just have him fly around calling himself Kal-El with some green incorporated into the suit in honor of his biological parents, or put them in different cities or whatever. There are a thousand ways that they could differentiate.