The CPU has shown some variation, but yes, it's the APU that has a ceramic clock source that isn't even close to the same among units. Apparently those ceramic resonators have a pretty high variation, even when new.

When byuu/near tried to find a middle-ground for the APU clock, the average turned out to be about 1025296 (32040.5 * 32). Some people have tested units recently and gotten an even higher average. They speculate that aging is causing the frequency to increase, but I don't really know if this is the case or if there really was that much of a discrepancy originally.

It does cause some significant compatibility issues, too, like with attraction mode desyncs and random freezes.