Hello Abhiheet242:
When a pump is assembled, deflection of shaft is checked to mechanical seal bores on case. If the shaft is not straight to bores then shaft is lower on one side increasing the possibility of rubbing against bores and other tighter clearance areas. Physical rubbing of shaft to bores can cause seizures (rotating and stationary parts can rub and get jammed). Lookup friction welding. It can cause vibration also.
Day before yesterday, I was working on a boiler feed split case pump where customer had requested clearance of 0.006” on vespel throttle bushing (high pressure side of pump). That is only 0.003” per side and imagine how easy it is for shaft to rub against bushing ID.
Why that specific number of 50 microns? My best guess is that they came up with this value by experiments and by examining where failures have occurred.