That is not really true. You usually have a couple of clock sources on a MCU, but the clock gets propagated down the clock tree and the source, and most of the times, the PWM has the same source clock as the CPU. Indeed, I think if you're before the PLL the clock is more accurate as in you get less jitter but the overall drift is the same. You might have distinct clock sources but you need a specific hw and a specific configuration.