Fastvid and the kind set P6 architectural registers so of course they won’t work on a 486. Otherwise it’s interesting to see how the motherboard jumpers did nothing.
But I’ve noticed something strange in your results: your 3DBench values are quite DX2–66-ish (with tight timings they should be 60+ with a DX4–100, at least my S3–864 gives such numbers and I don’t think the ALI card should be significantly slower. Wait a minute. I do have an ALI VLB VGA, I’ll have another look), I think I’ll check the rest too as I have the exact same motherboard on my test bench now.
Oh, about the VGA jumper: “50MHz” setting should mean that it uses relaxed timings for a higher expected bus frequency so it makes perfect sense that it’s slower that way. I don’t know if I can stabilize this system at 50MHz bus speed, though. Maybe with a DX-50 as I have no clue how to modify the DX4’s multiplier in this board. The manual is worse than the markings on the board itself :D