The point here being that it's going to be using the same chips already in use in Windows systems and therefore all of the pressure from the Windows side for faster/better chips will apply to Apple as well. I hightly doubt Apple entered into this relationship without some type of assurance that Intel would not make Windows specific chips.
I'm not so sure that Apple guiding the architecture is very beneficial to them. Apple didn't guide IBM's decisions either. Apple makes a great OS and that's all people should really care about.
Of all the benchmarks done previously by Apple with respect to G5 vs P4, the only ones the P4 did not win were tests where Apple decided to compile the code for P4 without using the floating point unit and such. But we really shouldn't get into that argument here. ;)
No matter where Apple goes unless they decide to start their own chip manufacturing plant, they will always be the minority. So why not go with a company who is actually pushing the limits on PC processors?