You, as the electrician, have absolutely NO CONTROL over the amps being drawn by the motor. Let it go... (I like that).
Load = flow in a centrifugal pump; less flow = less load if the head remains the same, hence the concept of the reduction in the intake. He could also trim the impeller, reduce the size of the pipe, it really doesn't matter how he gets there. But once the flow is reduced, the load on the motor will be reduced and the current will drop. Most likely, the pump OEM looked at the pumping performance spec, i.e. head and flow, and decided to do the job by running a smaller motor into the Service Factor rather than a larger motor. Standard Operating Procedure for 99% of pump OEMS I'm affraid; trim the cost to take the job low. But as you point out, the owners can write their owns specs, silly or not, and enforce them. That's the risk the lowballer supplier or contractor takes in bidding based on liberal spec interpretation and taking a chance that nobody will notice; he lost that bet. Again, not your issue, the pump suppler or mechanical contractor needs to deal with it in a method acceptable to the owner.
By the way, a motor with a 1.15 Service factor can be run at 115% of rated load, not 125%. Running a motor into the service factor is expected to put the motor sevice life and some performace specifications at risk, but NEMA MG-1 doesn't say anything stronger than that any more (it used to). Most likely the 125% you are thinging of is the maximum pickup point of the thermal overload proterction; separate issue.
Paraphrased (to avoid copyright infringement) from MG-1-1998
End users have every right in my opinion to insist that motors NOT be sized so as to run into the Service Factor, because THEY are the ones who will bear the long term cost of premature replacement. If they CLEARLY state that up front in the project specifications, then like I said, the pump supplier rolled the dice and lost. If they did not however, and are trying to enforce apresumptive expectation that was NOT part of the original specs, then they should bear the burden of paying for a change order.