Yes, you can edit the PFE spectrometer limit config values to match the PeakSight config values. They are different because every time you re-start the instrument, it does a self test on each spectrometer and will therefore come up with slightly different values which are then saved to the PeakSight config files.
Another philosophy is to set the PFE spectrometer limits to values that will generally always be slightly inside the PeakSight spectrometer limits when they are re-determined during the next instrument re-start.