I have a new spa with a Pentair Mastertemp 125. We have had issues with the heater running intermittently and making a very loud rattling noise. I've been through a long list of troubleshooting tips and it seems that flow is the issue. If I up the variable speed pump to 2300 rpm or more, the heater seems to work fine. At lower pump speeds, the heater fires, makes a terrible rattle for a few seconds and then shuts down. Checked filters and baskets; tried adjusting water pressure switch...no change.

You have already provided a diagnosis for the heaters problem... Low water flow. That IS the problem.
If you are going to be running your variable speed pump at an RPM lower than 2300, then you need to make sure the heater is in the OFF position. If you want to heat your body of water, then you need to ensure, that your pump will always be running at 2300 RPMs or more. There is no way you can go around this. you can calibrate your flow switch, or as it is more commonly referred to as the pressure switch, I know you stated that you have adjusted that already? but by doing this, it provides NO fix for the water flow problem. it only addresses the ability for the heater to come ON because of the lower water flow. But because of the low water flow, you're going to have moving water through the heater at a rate that is not sufficient.

Maybe that at lower pump speed the water is staying in the heat exchanger too long, and the rattle you hear is water starting to boil. The high limit sensors will sense the water temp being too high and shut down the heater. If it functions normally at high speed the issue is probably with the heater having problems with slow flow through the exchanger. You may want to consider switching to an electric heater where this would not be an issue. Just a guess without being there.