Don't forget that the 486 L2 cache, if there even is one, shares the processor bus with everything else. It's the same with a Pentium, but that 64-bit, 66MHz front-side bus gives a lot more headroom than the usual 25/33 MHz 32-bit 486 bus. And Pentiums usually have pipelined burst cache vs. plain direct mapped SRAM leading to better efficiency.
Part of the reason 486 PCI designs don't have much PCI bandwidth is because the entire system bus has (at most) slightly more bandwidth than 32-bit, 33 MHz PCI. But they also usually don't do DMA very well and that's really bad for a lot of PCI cards. Don't try a Verite in a 486 for sure.
Quake is actually designed around the pipelined Pentium FPU. I don't recall the details, but they coded the game to really leverage the Pentium architecture. It puts chips without pipelined FPUs at a major disadvantage (486, K5, K6, 6x86, Winchip, etc). Lots of people were up in arms over that, but it made sense for id to do it because Intel owned the market and they were pushing 3D tech to the limit and needed the speed. Assuming a 486 and Pentium are both equipped with fast vid cards and good mobos, the Pentium will be something like 2x faster per clock.
Of course, if you were really serious about Quake, you wanted a Pentium Pro. 😀