Different Ah is not an issue in parallel (it can be a serious issue when connected in series) but it is just not an issue connecting different capacity batteries in parallel to charge as long as they are same voltage. in fact any bike that has a battery that's made up of several strings of cells is already doing it as the charger doesn't know if its for example 3 x 2Ah batteries or 1x4Ah +1 x 2Ah.

BUT .....i think to have two BMS boards in the circuit fighting each other to control the chargers on/off switching is just asking for trouble, i wouldn't do it if only because i think charging might take forever because the charger would be trying to do almost all the work on trickle (green light on).