let me rephrase that...
the effective bus speed of a pcie is 2500mhz. the actual bus speed is 100mhz running at 25 peaks = 2500mhz.
so, for example(arbitrary numbers here for illustration only) if you have your fsb set to 250 (bus speed) and your multiplier set to 10 it gives your cpu an effective speed of 2500mhz, right?
its kinda like ddr ram.
i dont think bottlenecks should be near the concern that they are. i think if you overclock your processor to 2500mhz or a little above, you will eliminate bottlenecking unless you are overclocking the pcie bus (you can do that through ntune...helps 3dm06 quite a bit).