Pin dimensions on PCI Express card edge
The length of the pins is shown as 5.60 from the edge of the board.  Then there's a 1.40 chamfer at the bottom, which leaves you with 4.2.  You'd expect the chamfer to run through the pads, not have them stop short of it.
Yes, there are effectively two pads missing.  One might argue that it wouldn't be a centreline if it wasn't in the centre...


There are lots of PCIe templates provided by Altium, so you could have a measure of those if you can't just use them directly:  Here