IIRC you could. You would have to set up and calibrate the ECU first using full ATVs, then reduce down to you max desired thrust on the top end. I can not remember if the ECU wants to see max throttle for some calibration reason or not on each run, but Bob Price would know for sure. But if I remember right, you can set your max RPM, so why not do that?

P.S. all of the above pertains to the late model Bob Price designed, RPM controlled ECU. The older Electrodynamics ECUs were pressure controlled and much different. You could set a desired Max CP (Compressor Pressure) though.