When I make a five gallon batch, I start with 6.25 gallons in the kettle. After one hour, I have about 5.25 gallons in the kettle. After I transfer to the fermenter (through a strainer), I have just a tad over 5 gallons in the primary fermenter.
I lose about 9% per hour in the boil. That is my evaporation rate. Most people who do extract brewing just top off to 5 gallons in the primary, using water. That's absolutely fine. But when you do AG, you don't top off. You boil down to get 5 gallons. That's the difference.
Hops utilization is improved in lower gravity wort. That is, say you're doing a 3 gallon boil. You then top off with 2 gallons to get your volume in the fermentor. Well, in order to get a og of say, 1.050, your water that you'll be adding is 1.000. So your boiling wort is higher (maybe 1.070 or so) due to the dilution. (I didn't figure this all out mathematically, I'm just guessing)
That's why there is a difference in hops utilization.