Hi Steven_N
This schematic looked careless in places, and I had similar questions.
But fortunately I lived in the country where the connector manufacturer is located, which was helpful.
The GND of the FX23 connector is only connected to a few small contacts.
Schematic pins 105-108 seem to be intended for FX23 pins without contacts.
Also, pins number are inverted between schematic and FX23…
That is, 101- (schematics pin No.) = (FX23 pin no.)
I just created a PCB to break out PCIe signals and finished testing so there may be no mistake.
Some of my tweets.
https://twitter.com/OM2gpon/status/1452040223152500738
I hope it helps you!