Like many companies they make the same engine for different uses/markets/options etc. So the engine max output may be at 3600 rpm driving a generator, then also at lower hp in a tractor at max rpm of 3000, and in another tractor at a lower hp again. This is so they don't have to build 3 different engines. They will change or adjust the injection pump to get these variances generally, on petrol engines a different carburetor may be used or one may have occlusion gaskets in the air intake or butterfly stops etc.
However if they are both identical machines and both rated at 21hp I would first check the max no load speed of the engines. Get a digital non contact tacho and see if there is a difference. Of course as the lower power unit has alarms fitted, perhaps it ran hot previously and partially seized etc., and has had the extras fitted to stop it happening again. Go with the speed check, if the speed is correct, then check the adjustment on the hydros to make sure they are running at max output etc. Then perhaps a compression check as noted by JWR.
