Open the controller and look at the caps rating.
a 12V battery is usually 14.4V off the charger once settled for SLA
so 14.4, 28.8, 43.2, 57.6
Most 48V controllers are 63V caps /4 = 15.75 hot off charger per SLA brick. I'd expect a 36V cap to at least be 50V. So a 54V (48V labelled pack) is likely to blow 50V cap.
As long as you disconnect the controller from battery when charging and measure battery to ensure below the capacitor ratings.... you might do ok, other components might not have the same stretch as the caps but usually they do.
I think dnmun meant the LVC Won't cut off
48V pack high at 58 LVC around 42-40
36V pack high at 48 LVC aroung 31-33
So a 36V controller is looking for 31V cut off on a 48V pack so your battery is damaged by too low a discharge by the time it shuts off. This is because the 36V controller is perfectly happy still operating at 33V down to 32 or 31 LVC while that 48V pack would like to shut off above 40V.
if you use a 48V lifepo4 pack then you would wanna use a 36V controller so that the LVC of the controller does not shut it down since the 16S lifepo4 can produce current down to 32V. a 48V controller has a LVC around 40V so it will turn off before you can use all the capacity of the battery.
I think he was thinking using a 48V controller with a 36V pack would shut of premature to full usage of bat pack, as a 36V pack is high at 48V and the controller would shut off at 40ish while the batts is capable of going down to 31ish.
A 12V brick
14.4 full 10.5V empty
x3 for 36V pack
43.2 full 31.5 empty