Different motor power factor.I'm unsure how much it will effect the numbers, but historically I can testify that submersible pumps tend to pull more current than the equivalent conventional frame motors. For example, I have a data sheet on a 40HP GRUNDFOS pump that shows a 40 HP pump with a 64 FLA compared to 52 amps from 430.250
I am led to understand that the windings are much different do to the reduced diameter to fit the well.
In the case of a VFD, differences in efficiency will change the input current for any given load. Usually the current taken by the motor is higher than the input current to the VFD.