I never have. I do know that if you plug a PCIx (different from PCIe) card into a PCI slot it will work, but at a much slower speed. This is because half the card is hanging out the back of the PCI slot. I think if you plug in a 66MHz PCIx card into a PCIX 133 slot, it will slow ALL cards down to PCIx 66.
The only thing I can think of as to what he is talking about is PCI video cards are not fast. Depending on what PCI card you have, the onboard is probably faster. This would make "the computer" slower if you use the older PCI card, as the graphics wouldn't be as fast. If you aren't gaming however, this won't matter.