A lot of people put their chargers in a top or side box on the back of their bike. You then do not need the belly pan.
This set-up also provides you with a nice place for the Inlets (the socket where you plug your charge cable in) and a handy place to store your charge cables when driving. In this set-up you most probably need a fan to cool the charger(s). With the belly pan that is not needed because the pan acts like a heatsink.
If you want to continue using the stock charger, which I understand you would want to, then you could try to get yourself a V2 or V3 version of the brainbox, these do not have/need a CANBUS connection to the bike. A positive side of maintaining the stock charger is that you can use that one to put the bike in charge mode. Without the stock charger you either need a V2.5 brainbox or a special AUX Anderson set-up with a resistor and a switch to put the bike in charge mode.