There should be no draw back. The goal is to have the least amount of pressure drop from lift pump to cp3. Everything that involves flow will have a pressure drop. you will have less pressure drop using a 1/2" line to the 3/8" orifice than using 3/8" all the way.
It all really comes down to...
The calculator is a guess, doesn't mean your overall setup will cut that time. Also, corrected dyno numbers are misleading on the track...you can't correct a 1/4 pass if conditions were unfavorable
check this view out! After seeing this vid, I bet there was quite a bit of puckering going on as you crested that hill!!
http://www.youtube.com/watch?v=fCoxtkPKotU&feature=relmfu