This is so weird....like the third thread that's had a 4-5 month delayed reaction.
Anyway, it's boggling to me because you're essentially wanting to take away something that makes superhero comics unique. You may have some shared universes in other mediums, but they tend to be pretty light or just for flash (like video game fighting crossovers). It's like Alan Moore said in an introduction to one his Swamp Thing trades: It's a place where Superman can exist with Swamp Thing and Etrigan and still feel completely natural if done the correct way (paraphrasing, obviously, but that's essentially what he's saying, which is your reasoning for why it doesn't work).
I guess it's also boggling to me why you can't just separate this **** yourself. Why can't Superman contrast between the normal and fantastical? Simply because he lives in this shared universe? Why does this shared universe always be self-referencing itself? Why can't we just say, "This is a Superman story that does that, where we won't have to worry about any of the other heroes for now." I mean, why? It's like people who ask, "Well, why doesn't Superman or the other metahumans just clean up Gotham for Batman in 5 seconds?" And the answer is the question, because why would you want that? And why do you feel it's needed to be addressed. Just like it lay. Basically, when a shared universe can be utilized, there's no reason it shouldn't be, but when it doesn't need to be, then why do you have to poke at it and go, "But....but....but.....but....WHY!?" It's like Grant Morrison says, "Why is it like that? Because superheroes aren't ****ing real!"
Now, I'm not saying there aren't ever any legit problems. I think some of the stuff that The Batman brought up (the whole JSA integration stuff especially) is perfectly valid. But speaking generally, I just don't see why you'd want to cut out one of the most interesting and fascinating aspects of superhero comics. I mean, honestly, I don't see how people who question that kind of stuff can even stand to read comics. You're dealing with the most unrealistic, fantastic concepts of the modern age, you just have to tune your reality to theirs, it seems to me, anyway.