ok i may end up way off base, but here it goes...

Remember, the trap speed is secondary, your main goal is to get there as quickly as possible, not as FAST as possible (I know it sounds stupid, but it's accurate)
Don't get me wrong, MPH= HP which will help you drive around people, but it's not the main measurement of a drag race.. your ET is..

you wan to go through the traps at the top end of your power band...

a higher (numerically) gearing will get you into your power band quicker, but you will also run out the other end of the power band much quicker as well.

If you short shift your earlier shift points I believe you are right that you will most likely be running slower going through the traps than if you ran each gear all the way out. You're motor will have to work much harder if you shift into the top gear below your power band and you will not be accelerating as fast because of this, but by short shifting you are going to need to extend the 4th gear longer than what you normally would. THis most likely being outside of your power band, again you're car will not be accelerating as fast since your HP levels are most likely falling off pretty quick...

soooo..
short shifting 1st 3 gears = winding motor up higher through traps
extending shift points in 1st 3 gears = below RPM power band through traps
either one can produce either slower or faster mph through the traps depending on conditions, etc.

Shift at the highest point in the power band in which your car is still making power gear your car to keep it in the power band based on your motor's performance/trany combo. (via gears/tranny/tire size, etc)

i.e. i've got a c-4 (3spd)
4.56 gear 1st and 2nd I shift around 7800, go through the traps about 8k..
hope I wasn't too redundant as I'm sure you know most of this, but figured i'd throw it out there...