They did take out 3DMark03 optimizations. Dunno about 3DMark2001 but with nVidia it's more serious since its been confirmed they drop their AF quality in UT2003.
The funny thing about 3dMark03 is that it's all a bunch of crap no matter which way you look at it. You can easily say that ATi took their optimizations OUT OF THEIR DRIVERS, but since they are also part of the 3dmark03 beta, their optimizations could just as easily still be in the PROGRAM ITSELF, a luxary that nVidia doesn't have.
EDIT: Looked at the BEyond3d Ansio article and what a surprise, ATi's drivers also won't perform Trilinear filtering while on Quality setting either...