That looks really cool and the level of detail is impressive!
Much nicer than I was expecting!
I built something similar a few years back, except it was an NTP appliance rather than a nixie clock, and I have yet to pick up PCB design skills so the whole thing was separate boards and breadboards with wires flying all over the place. When I got into amateur radio I realized the crazy amount of noise it was putting out, and I needed the bench space anyway, so I took it apart :)
But it was a broadly similar architecture, with an SA.22c in place of the SA.32m, the same NEO-M8T (okay, actually an EVK-M8T evaluation board), and an Arduino Due clone taking the place of the FPGA and Raspberry Pi. I connected the Rb to the external-clock input of one of the Due’s timer/counters, used that TC block to generate a pulse-per-second, and fed that PPS into the M8T’s external interrupt pin, and used the timestamps from that to drive my PLL. The digital PLL talked to the SA.22c’s DDS controller, much like this design — no analog control anywhere.
I started off using 10MHz from the Rb directly to clock the timer on the Due; later I raised it to 31.25 MHz using a TAPR Clock-Block (the SAM3 chip requires an external clock to be less than 0.4 times the frequency of the main clock, which limits things to 33.6MHz, and 31.25MHz comes out to a nice number of nanoseconds per tick), then I dropped it back to 10MHz, then I switched to 30MHz directly out of the Rb (without the Clock-Block), after improving my code to no longer require a “nice number of nanoseconds per tick” :)
I also had nice grafana dashboards, and I managed to keep my tick within a couple 10s of ns, which is about as good as you can really expect… and in any case, using it as an NTP server degraded the accuracy to the 1 to 10 microsecond range anyway. But, I could say I had an atomic clock in the house!
It also would have made a great 10MHz frequency reference if it wasn’t so busy spewing noise into the environment, but once I found a need for that, rather than rebuilding mine, I just bought a Leo Bodnar LeoNTP, which is a tenth of the size, uses a tenth of the power, and is RF-clean.