|Quoting GST (Reply 1):|
The longer crown will have marginally (and this is very marginal indeed) greater surface area and thus friction drag. On the other hand it may make for a more favourably consistent change in cross sectional area of the aircraft as you go back, so for highish transonic cruising this may be better. I doubt there are released figures that can let the layperson (and competitors) check this too carefully mind, so you'll probably only get theories here.
The history of the SUD (Stretched Upper Deck):
-Boeing develops 747SP, discovers during testing that fuel consumption during high mach cruise (~0.84M and above) is much better than predicted. This turns out to be because having the upper deck terminate just before the wing root creates a previously unknown area rule benefit.
-To capitalize on this discovery (on non -SP's), Boeing develops -300 model, and even sells some SUD modifications (for -200's and even -100's) to the likes of KLM, ANA, and JAL...
-400 passenger model available as SUD only
Of course, the 747-8i carries on the legacy of the stretched upper deck, including more favorable fuel consumption at higher mach numbers.
Non-converted freighters don't use it, because #1, it adds weight and #2 the upper deck floor impedes on cargo volume (apparently, some freight operators load out the 747 floor to ceiling). The (slight) aerodynamic benefits of the SUD don't outweigh the disadvantages in this case. Passenger operators like it because you get more seating upstairs...