I suspect available RAM also makes a notable difference.
My A4000 (50MHz '060) with the standard motherboard RAM (2MB Chip/16MB Fast) was very slow (3.1.4.1); but my A3000 (25MHz '040) with 2MB Chip/6MB Fast--and the 256MB BigRamPlus--was significantly faster.
Both are running 3.1.4.1, the 4000 has a PicassoIV and the 3000 has a CyberVision 64/3D; both using P96.
Need to order another BigRamPlus for my A4000, but they're out of stock as of this writing.