Damn. Just when I thought ZUN's musical genius couldn't get any more awesome, he breaks out the two-layered songs. Though I must say I'm a little disappointed that you'll never be able to hear the "true" versions in actual gameplay.
Yes! So it isn't just pointless fanboy fantasizing. Combining the 2 halves together truly gives you the WHOLE song, the "true" version! It's like ZUN's playing some kinda twisted audio version of the Mega-mega-mega-man joke on us all. -_-