Thus far I've seen no story that played around with the concept of parallel universe counterparts running around, they'd have different names of course because "twilight sparkle" is a stupid name to have in America. So in the cliche opener off a giant bubble emerging in the ocean, how would their human counterparts react?

7253978
At the point where the various characters are visually realistic enough to fit into everyday America, combined with a more down to earth name change, I don't think they they would even be recognizable as their pony counterparts anymore. Even if they met, they'd most likely write of any similarity in personality as coincidence.

7254113
While true, what I want to know is how they'd react to the whole scenario. Besides we can at least keep nick names, for instance if RD is in the air force her call-sign could be Rainbow, and the lightning bolt painted on the tail of the plane. Pinkie and Applejack are fairly plausible nicknames imo

7253978
Twilight would be fascinated, and perhaps afraid.

7254590
I imagine that she'd quickly be put to work studying it, though it's only headcanon that she'd pursue theoretical physics