There's really only two or three options with a heater that is displaying an exhaust temp that high.
Sooted, (typically) calicified exchanger, or a bad temp sensor.
Essentially, the exchanger is just copper tubing with copper fins for more efficient thermal conductivity.
If the exterior of the exchanger is coated in soot, the soot will act as a thermal insulator, causing most of the heat from the flame holder to escape via exhaust. If the interior of the exchanger is coated in calcium, chemical residue, algae, whatever the case may be, same effect will occur.
Normal operating parameter on the heater is going to be 290-330 degrees F, anything higher is a sign of some sort of insulation on the exchanger preventing proper transfer of heat.
Unless it was a bad board, which I have honestly never seen fail in such a fashion that would cause the heater to read the exhaust as hotter than it actually is (normally, the exhaust will read as 80/40, and not really move from that). The SFS could be ohmed out, which should read 3.8-4.2 Mohms to be considered "good".
Seeing the report from the chemical analysis, that does indicate there would be likely some interesting things going on internally due to chemistry of the system. Phosphates, by and large, are bad for your pool. Being a food source for algae, removal is advisable, but obviously if you have a algae situation you're wanting to add algaecide and shock and regular chlorine additions in order to mitigate that problem, but part of the equation ends up being removal of the food source.
Typical gas tends to be 8-10" WC static, no more than a 2 " WC drop when firing for natural gas. But the spec is 4-14" WC technically. So, your burn will not be ideal, but it shouldn't be problematic in the normal life expectancy of the heater. I have never seen a heater exhibit a problem as you've describe, with too large/powerful of a flame. If the gas line readings are accurate, that isn't the issue at all.
Trying to understand the situation as it is presented, but the principle of the heater and the behavior being exhibited aren't meshing well at all. I'd be very interested in knowing who the service team from Pentair is, and what their determination is because it isn't clicking as to what the cause of the problem is here.