> whether there exists an external "system clock"
I'll ignore your analogy with a CPU, which I don't think is apposite.
Whether there's a 'system clock', a sort of reference clock that can tell you how fast time is passing, so you can calibrate other clocks against it, seems to be the same category error. As far as I can see, either time is all there, all at once; or one second lasts exactly one second. (I've perpetrated the same category error there, because a second doesn't 'last' for some period of time; it just is).
[Edit] That's not very clear. I mean: if you are measuring a distance, you use a calibrated ruler. If you doubt the calibration of your ruler, you might recalibrate for precision. But you don't have a clear idea of what one foot is, it doesn't make any sense to ask whether your one-foot ruler has grown or shrunk; how would you tell if the purported 'fact' is true or false?
And if some fact about the Universe means that it has grown or shrunk, how would you tell? If you can't in principle tell whether a 'fact' is true or false, it follows that the 'fact' isn't a fact, because it has no effect on anything.
See Russells Teapot.