Hi,
Why not:
2 similar batteries in parallel (same cells better separation, larger case)
Both PCB´s in separate chamber
Same (revised) BMS
Same charger (One for both batteries, "switched")
Improved sensing to shut off (battery) when one cell "starts" to fail
1 BDM per battery (MAIN)
Sturdier and vented (to outside) case.
Located nearby current positions (cable lenght optimization)
Total 4 batteries (2 MAIN, 2 APU)
Result: Better dependability, fault tolerant, graceful degradation, less fire risk, planes flying sooner (probable) and safer also because (batteries) could be derated.
Weight penalty: Aprox. "1 pax"
Please, BOMBARD it!