[vector1]

i would say yes, the program compensates for the exhaust port length using the valve face to mating surface, so the measurement of the primary pipe is face of the exhaust flange to the exit at the merge collector. in your case 3.2 was used for the exhaust port, all measurements would be centerline.

keep in mind this is a 427 with likely similiar specs as your engine, your cam & a few other things might move things slightly.