The CVs do not change the PWM voltage PEAK. At least for CV5, max voltage, you can think of it like a physical stop on the throttle knob - you can't turn it any higher than that.
As you start from speed step 1, the pulse being sent to the motor is very narrow. Motors are inductive, thus they react to the average voltage, not the peak. The average of a very narrow pulse of say 15 volts is very low. As you increase the throttle, the pulse gets wider and wider. As it gets wider, the average increases, and the motor responds by speeding up. The peak is always the same 15 volts or whatever. Setting CV2 controls how wide the pulse is on speed step 1. Setting CV5 controls how wide the pulse is on the highest speed step, 28 or 127. Setting CV6 controls how wide the pulse is at the middle position, 14 or 64.
Say you have a loco that at full throttle runs at 100 mph, but the prototype should only go 60. As you turn the throttle from stop to max, you have a range of 0-100mph. You adjust CV5 until the loco goes 60 at full throttle. Now as you turn the throttle from stop to full, you are controlling a speed range of 0-60mph. With the same number of speed steps. So each step is a smaller increment.
CV2 is alittle more tricky. This is more dependent on physical characteristics of the loco than any conformance to prototype operation. A motor will require some minimal voltage to turn. Depending on the motor, that may not be reached until you are on step 10 out of 127. This manifests as a 'dead' area in the control where you turn the knob and nothing happens. By adjusting CV2, you can set the decoder so that the motor sees the bare minimum it needs to run on the very first step of the throttle. Again this also expands the granularity of the controls - before adjusting, steps 1-9 did nothing, the loco started moving at step 10. Now, the loco starts moving at step 1, and 1-9 all control the speed.
CV6 is of more use to matching multiple locos across the entire speed range (once you have the start and maximum speeds matched). Or configuring a loco by its use. FOr example, back in first gen diesel days, a lot of railroads used the massic FM Trainmaster for commuter trains. Not because a 3 or 4 car passenger train needed 2400HP to pull it, but because commuter trains by nature stop at every station and they need to get moving after each stop. The faster they can accelerate, the tighter schedule they can keep. If you make no adjustment to CV6, the mid throttle position will result in an average voltage to the motor that is exactly in the middle of the voltage at step 1 and the voltage at the top step as set by CV5. Speed increments as you turn the knob will be in a perfectly straight line between stop and top speed. If for example CV2 is 10 and CV5 is 210, the range is 200, and CV6, if not programmed, will behave as if it is set to 100. Right in the middle. If you set CV6 to something higher than 100 in this case, then the first half of the throttle will result in a greater change in speed than the second half. Say you set it to 160. 160 is about what 3/4 of the throttle would have been (keeping with the example numbers - if it goes from 10-210, the range is 200, 75% is 150, and there is that offset of 10 for the starting voltage, this is how I am coming up with 160). SO now when the throttle is at half way, the loco will be going 75% of its top speed, not 50%. This is more like that commuter train loco, picking up speed quickly after it stops. Likewise, you can do the opposite for say a switcher. With the same settings in CV2 and CV5, it may accurately represent a 60mph top speed, but even if capable, a switcher would rarely tun that fast. so you might set CV6 to 60. 25% of 200 is 50, plus the 10 offset again. Now, when the knob is at half, the loco will only be moving at 25% of its top speed instead of 50%. You still have half the steps on the throttle to get from 0-25% speed so you have very fine control over the loco at the lower speeds, perfect for coupling to cars without smashing them down the track.
That is about the best I can explain CV2-5-6.