For Heater charge , we have two pumps ( Pneumatic and electric  diaphragm pumps both are motor driven) . One will be running and another as standby which will be kept in autostart mode . The standby pump starts in autostart mode when the discharge header experiences low low pressure.We have sufficient NPSH margin ( more than 2 metres) at rated conditions and nearly 0.6 meter at 120% of the rated flow. The rated point is nearly 82% of its BEP. I would not disqualify a pump selection based on a transient condition that might last for a couple of seconds and only during an unplanned auto-start scenario.  I am more concerned about the basis for the NPSH margin at rated conditions.  I don't know if everyone does this the same.  Our specifications require that the pump have an NPSH margin at rated flow of about 1 meter (for hydrocarbon streams).  But, the calculation for NPSH available is based on the suction vessel level at bottom tangent or bottom nozzle.  This makes the calculation inherently conservative.  Since the normal operating liquid level might be more than 2 meters higher than this reference, we have an actual NPSH margin much higher than the calculation would suggest. 
Even if you are using actual running level for the NPSH margin, I would not worry about a couple of seconds of low margin (or negative margin) operation during an unusual and rare operating condition. 

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