I believe it does. But it's just not reflected on iTunes. So, most people will just being seeing Roar at #1 and Applause lower even though it's probably actually selling more based on pre-orders. This is assuming that Applause doesn't sell enough solo versions to trump Roar. It could!
However, a #1 position on iTunes definitely is great exposure for a song and it'd be a shame for Applause to miss out on that just because people are pre-ordering the album instead.
Ain't nobody checkin' for the amount of pre-orders or first week sales or chart position, but they do check iChunes.