OK, that's that then.. I'm gonna go with a combination of exaggerated wind effect on the ball and exaggerated hang time from backspin. Those two things would make fly balls carry a lot more than they should.
I would design those systems to be easily tweaked by changing a few variables, but I don't know how they designed it. Also, I don't know if those variables can be altered at this point since the game has already been compiled..
The reason I'm thinking it's exaggerated hang time from back spin is because I've seen screen shots of people's monster HRs and the hits have high apex heights but drawn out apex curves usually seen in line drives (or any HRs with lower launch angles). Hits with high apex heights have sharper apex curves (they drop more sharply) in correlation with higher launch angles.