String-thru feels worse on my MIA Jazz IMO, might be my imagination, but I think action doesn't feel as even.
Doesn't get enough tension to solidly push the E string to the saddle either if its not one of those taper-wound E's
if the string is touching the saddle and the nut and is tuned to pitch it shouldnt matter if the string is attached in space it should be the same..... but as i said below i know guys who swear by putting the lower strings thru the brdge and the D G thru body....try that