For what it is worth, I of course considered buying the Noctua step-down converter NA-VC1 but it has a four-pin design, while the Ampeg board has three pins (only two of which are used by the stock Ampeg fan). So using it would have necessitated further work. (But then I discovered that the board seemed to be delivering only 12v.)
Regarding voltage: I checked the voltage on the board many times and never saw anything other than ~12 v. I have never heard the stock fan or the new fan increase (or decrease) in speed. So I have never experienced anything that looked/sounded like the Ampeg delivering more than 12v to the fan. But obviously that information alone is inconclusive.
I do not know enough to extract any useful information from the diagram that agedhorse posted. But if I knew that the Ampeg would, under increased thermal load, send > 12v to the fan, I would then become uneasy about my mod. Any suggestions (besides the obvious "let it get hot and see what happens") about how it could be determined whether the Ampeg does that? (Or maybe it's already been said above that this is known, and I didn't quite understand; if so, sorry for the trouble.)