I'm pretty new to this as well but this is how I understand it:
Higher voltage = higher top speed. So the 48V kit will allegedly have a higher top speed, unless there is a speed limit built into the controller.
EBike Beginners info - Endless Sphere Wiki
The different AH ratings (20AH vs 11.6AH) are a measure of capacity. More AH = longer distance you can travel on a charge. You can multiply the voltage by the AH to get Watt Hours (Wh) for that battery.
48 * 20 = 960Wh rack mount
36 * 11.6 = 418 Wh bottle battery.
My ebike does about 18Wh per km if I'm going fast without pedalling much, so my range would be:
960Wh / 18 = 53kms on rack mount battery.
418 Wh / 18 = 23kms on bottle battery.
The AH do not relate to "too powerful" or not. So assuming the motor supports 48V (I think it does) then its fine.