This assumes the 43v controller is limiting the amps further to get the same amount of watts. Do we have any idea if there is actually two different models or if one just has 36v firmware that also allows more amps? And if they are the exact same motor if both bikes are geared the same the lower but more amps 36v should in theory give slightly more torque with the higher voltage giving a slight rpm increase. Reminds me of the uart bafang motors where you could get a 48v model and stick a 52v battery to get more power. Of course they then released a 52v model but it also lowered the current to match the watts of the 48v. With then later firmware unlocking the full amps with 52v software.Power is equal to voltage x current. So if you have a 540whr battery/36v the current is 15a but a 540whr/43=12a so the 43v needs to handle less current than the 36v battery.
It is a little easier to find 36v external batteries than 43v.