You need to be able to shut off all voltages coming out of the front pack and the rear pack for safety reasons.
That precludes running 96 wires willy nilly all over the car to a single BMS, since those wires always have voltage on them and are usually not fused. So, you'll need a BMS master in one box connected with galvanically isolated communications to a satellite BMS in the second box.
You also need two contactors inside each battery box. One for plus, one for minus of its HV battery connection.
Interbox HV cables should be run separated, so a responder with a chop saw does not melt the sawblade with 2000 amps running through it. Ideally protected from road debris damage (including innocent-looking rocks, gravel, dropped car parts, and traction grit).
HV charge port cables need to run to a box with 2 more contactors applying voltage to the HV battery in the proper sequence if you are planning DC charging.
Depending where you live, you likely will need a coolant heater in the loop for the batteries as well.
Any heat source connected in series will heat the downstream heat source. So, no, you will not be equalizing the temperatures.
You can run the rear battery box's coolant loop through the motor (not the other way around) if you want to be frugal about number of loops.