In July 2022 Sukhdeep sent me this link to an announcement on Reddit.com from somebody who had soldered in a PCIe socket on a standard t620 and had plugged in a NIC and used it with with pfsense. You need to scroll through the comments for the detail.
A couple of answers from the comments that addressed my immediate thoughts:
If they leave the socket off they usually leave off other associated bits and pieces.
I did see it was missing some stuff, thought I'd try it anyways and it powered on fine. Might look into what they were for.
In the past I've struggled clearing pcb mounting holes just to fit a SATA data socket.
What took me 4 hours though was clearing the holes as most had solder from the factory.
..and there is some general guidance:
I'd have the board clamped vertically while I heat up the top side of the hole then suck out the bottom with the solder sucker. It works for most of the holes and in my case you could see the solder bubble out so it made finding the right one a lot easier.
There were some holes that just would not melt for what ever reason, they needed some poking with a piece of copper wire (from cat5) with the hot iron on the other side. Others I used the copper to suck up the solder and one hole I forced it through and lucked out.