On the mystery voltage regulator: most OCXOs also provide a regulated reference output on the pin that's marked N/C on this device. This reference is important because the tuning voltage is scaled relative to some reference voltage, and a modulation in that reference voltage can be seen as an out-of-phase modulation in the tuning voltage. Hence, bringing a pristine reference out of the oven is the cleanest option. Second best is to place an external regulator close to the oven, as they've done here.
That's what I use in the GPSDO in one of my projects. The internal voltage reference powers a 10bit DAC that we dither to tune the OCXO. If the microcontroller has a voltage rail just for it's internal DAC, that would be the best way to run it. You could drop the opamp and voltage reference from the design and just keep the RC filter.
The opamp would still be a good idea no? That RC filter output will be very susceptible to noise and we wish the OCXO tune input to be as stable as possible. When I built one of these a friend had me route the opamp output as a guard ring around the entire DAC to VCXO tune net.
I'm not sure: I remember seeing comments in the past about crappy Vref outputs of OCXOs (when compared to external Vrefs) and just today, I saw another such comment though I don't remember where either.
I've studied quite a bit of GPSDO schematics, but none of them are using the internal Vref. Though that maybe because these designs allow for different OCXOs, some of which don't have a Vref output.
"Lastly, I'm not going to use the Oscilloquartz reference voltage to power the frequency setting circuit. It seems the logical thing to do, but this so called reference voltage is anything but a reference voltage. They are typically created by using a zener (reference) diode like the TL431, but that is simply not good enough as you will see."
...at least that's my best guess.