Critical Issue
Compared to the standard full compilation flow, you might see a slight difference in Fmax when you compile your design using the Per-Stage Compilation flow in the Quartus® Prime Pro Edition software.
The Fmax difference is caused by random compiler variations, equivalent to changing the Fitter Initial Placement Seed setting in the Advanced Fitter Settings dialog box. If your design does not pass compilation consistently across different seeds, optimize your design to add more timing margin so that it can absorb these random variations.