I didn't really notice because there was a fair amount of slack before I started winding them. When I realized it was clearly going to sit in the nut-slot, I top-loaded it. I was a bit surprised because the silk on the other 3 strings easily cleared the nut while going through-body.
I had no problem whatsoever in getting the intonation set. In fact, it seemed so spot-on after a few minor tweaks that I said to myself, "Wow. THAT'S what I'm talkin' about!"
That said, I was playing it a for awhile earlier this evening and I'm still not totally happy with the tone of the E string. It sounds much better than when I strung it through the body; but still seems to lack a bit of the punch that the other 3 strings have. The old Chromes I took off sounded perfectly uniform across all of the strings.