The throttle is opened mechanically at a constant rate across the length of the pull, keeping it consistent. You're correct that a hand-operated throttle would skew the results.
actually what you want is to jack the throttle open as fast as possible to wide open throttle. Mine is going to use spring triggered opening and servo forced closing. You want the motor to pull as hard as possible on the flywheel from the bottom to the top. With an inertia dyno the whole premise is to determine how fast the engine can spool up the flywheel so instantaneus throttle opening is required.
you can tune the engine using exhaust temprature, it will be in the 900 degree range, obviously it will take several passes to find the window of optimum power.