IT IS DONE!
BIOS v2.08 with 2011 boot block updated to v3.85 with 2013 boot block.
Tried both the CH341a and Raspberry Pi 3 but only had luck with the RPI3 - however this could be due to the SOIC16 clamp cable as I only got a good clamp after several tries on the RPi3.
I made one mistake in forgetting to update to v3.85 before flashing the bootblock, resulting in the somewhat cursed result of a 2013 boot block on a v2.08 BIOS (from 2012, so this combination of BIOS and boot block is never meant to happen). But no worries, the Z620 still booted, and I made a FreeDOS liveUSB to use HP’s BIOS update utility and update to v3.85.
I also completely messed up the pinout on my first go with the CH341a and the chip seems fine. My CH341a is also the type (black PCB) to use put out 5V on the logic pins no matter what, so my SPI chip definitely experienced some errant bullshit with seemingly no permanent effects.
I don’t have a Xeon E5 v2 to test with, but at this stage they should all work with no issues. Waiting for the high core count ones to get extremly cheap on ebay 
I’m currently writing up a guide, will post in a few days.
Here’s some pictures of the process for now:
Do the BIOS update to 3.85 first (unlike me)
Unplug the motherboard power connectors to minimize passive load on the SPI programmer and decouple from the PSU.
When I finally got a good clamp it was with dangling RPi3, so I let it dangle for the 2-3 hours it took after that.
I was worried about the length of the jumpers but in the end it didn’t seem to be an issue
On the whole I think this was still worth it over desoldering or lifting pins
