Hc32f460 MCU Clock Speed Issue/Bug

FWIW, I do not think this is the case.
Regardless if 200 or 168 both are fast enough to drive your speeds and if more steps than available processing power are generated, then Klipper reacts with Rescheduled timer in the past

This would be a catastrophe. The steps and their timing must never relate to the the MCU freq. The total number of steps over all steppers depend on the processing power / clock speed.
You would not want your steppers run 4x faster on 200MHz board compared to a 50MHz board.
Also see above link under “Benchmarks”.