Almost always, practical physical and economic constraints result in pumps operating with less than perfectly ideal suction head conditions.
NPSHr increases in a non-linear manner in proportion to the difference between the actual flow rate and the BEP flow rate. The NPSHa increases for flow rates below the BEP flow rate thereby inherently at least mitigating some of the NPSHr burden from off-BEP operation. The potentially more serious situation usually involves operation at greater than BEP flows where NPSHa drops as NPSHr increases. Since the pump's power requirement usually increases quite rapidly as the flow rate exceeds the BEP flow rate, pump's don't usually operate very long is this mode anyway.
Sometimes, a pump's NPSHr is based on 1% rather than 3%, so it is usually a good idea to be sure what standard is used for a particular pump's ratings. Also, it is common for a pump's ratings to be based on operation at a constant shaft speed (often but not necessarily a synchronous speed such as 1800 rpm or 3600 rpm), Sometimes, smaller, direct-connected pumps may be rated based on operation as powered by their standard induction motor so that some modest variation in shaft speed may be included in the pump's rated performance curves. Usually, these small variations in the rated performance are not troublesome, but I have encountered situations where problems of apparent performance deficiencies have resulted from a misunderstanding of the manufacturer's rating system.