Autoflight New Zealand does not clean their gears, or housings. There will be lots of dust left inside from the machining, as you know.
However, until you run the PSRU with a full load on it (propeller installed), and at high rpm, you will not accomplish much in the way of break-in of the gears. Thus you will not hasten the clean out of the fines and other metal that is inside. Realize that you will continue to "make metal" for a number of hours. How many? I do not know.
When I did my first oil change, the oil was a mild gray color. After letting the oil sit in the drain bucket a couple days, it all settled out to the bottom. It was shocking to my eyes, but it was explained that this is completely normal for a new PSRU.
Yes, I would change the oil at two hour intervals, 3 hours at the most for the first 20 or 25 hours. Oil is relatively inexpensive, especially with an airplane that is costing 200K and up. And send it to Blackstone Labs for analysis.