The gearbox on the the engine itself is not a CVT- it reduces the engine speed at a ratio of 3:1 meaning that that the output shaft is turning 1/3 the speed of the engine. That is fine if you just want to run that to the rear wheel, but there will be one, fixed ratio- now additional ratios. Why additional ratios? Because the 3:1 reduction is fine for cruising, but very, very sluggish at lower speeds- takes for ever to accelerate. It would be so much nicer if there was some way to have a lower ratio so the engine could turn faster, in its power band, at a slower sped, then some way to change ratios to and intermediate range to continue decent acceleration, then a final ratio to cruise at with the engine not screaming at a very high speed.
Bingo- the 3 speed transmission. Think of it this way- with that three speed, you have the equivalent of 3 rear sprockets- something like an 70 tooth for acceleration at a lower speed, a 60 tooth for intermediate and a 48 tooth for cruising. However, you get all this just in that little three speed hub.