"..and so, you see, son, that's just an alternate universe Batman...not the real Batman at all."
"Um, Daddy...You do know there isn't a 'real Batman,' don't you? Maybe you should come to school with me today so that my teacher can explain to you about make believe."
But, seriously, Brett was talking about "the meta level" or symbolic meaning, and I'm not sure the symbolic meaning changes that much, especially (but not only) from a child's point of view, whether you label a story "Prime Earth" or "Earth Two."
Personally, it's Ok with me, because I think the symbolic meaning is that even flawed people like Thomas Wayne can be inspired by heroes and can try to do better things with their lives (even if they still are far from perfect).
And in Wonder Woman's case, I think the symbolic meaning has to do with the hope of a hero coming out of a bad situation and showing everyone a better way. (And I very much agree with what Vanguard is saying along those lines.)