I was once told that FM doesn't really cover the low end frequencies... ? don't know if it's true. if it is, that's a definite reason to not go this route.

Depends on your definition of "low end", and depends on what the factory stereo produces.

If you can listen to the radio on your factory stereo and you like the way the bass sounds just fine, then routing the empeg through that same system is going to be just fine for you. Most factory speaker systems can't produce extremely low frequencies, so this isn't really an issue for anyone who's going to be using an FM modulator anyway.