I'm pretty sure that most controllers were pre-set by default to 24V, which allowed them to be used with 24, 36 or 48V. Your controller will run fine on 48V, as the voltage setting is mainly for the Low Voltage Cut-off, which is used to prevent the battery from becoming overdischarged, but most ebike batteries nowadays come with their own Battery Management Systems
(BMS) which also does the same job. So unless you're using Sealed Lead Acid
(sla) batteries or a Lithium Polymer
(LiPo) pack there is not much point in changing the voltage setting.
Saying that, I use a LiPo pack which I often change between 25.9V 10Ah and 51.8V 5Ah for use with my Pie. Although I don't have a
BMS, I do use an external plug in battery monitor unit which beeps if the voltage starts to fall too low.
Alan