The controller electronics is the limitation of the battery voltage so if you change the controller. That controller voltage will define your max voltage.
You can run some motors with only the thick phase wires connected if the controller can work in sensorless mode. Or virtual hall-sensor modulation* you could say with other words.
The protection from where the cables comes out is not the most important. Rather everything else and when all is finished you but some glue, melt glue or silicon in there so no water gets in.