Why does 64 bit PCI have 2 notches?
Compatibility with 32-bit slots

There are no electrical reasons for the notches, but having at least one notch makes everyone's lives much easier. With that out of the way, the reason for the notches in the 64-bit card is for compatibility with 32-bit cards.


Semi-inserted PCI-X card in a 32-bit PCI slot

32-bit cards in a 64-bit slot

A 64-bit slot can accept 32-bit cards, so the slots must be designed with the same properties. Since the question is not about 32-bit cards, we can simply accept that the 32-bit slot has notches.

A 64-bit card designed to fit in a 64-bit slot must have notches in the same place as the 32-bit cards, for this reason.

64-bit cards in a 32-bit slot

As for the rightmost notch. It could technically have been left out, and the connector could just continue on. The "problem" is, again, compatibility with the 32-bit slot.

A 64-bit card will often (always?) work well in a 32-bit slot, you will just not get the maximum bandwidth. The notch in the edge connector is necessary for the 64-bit card to physically fit in the 32-bit slot.