6 v GC batteries versus 12 v lithium deep cycle batteries

The internal BMS should be cutting off the discharge at low voltage before damage is done. Same as the top end. If you are consistently going into the lowest 20% I will recommend more battery or at least charge closer to the top. Then you end up top balancing. It all works out fine without worry.

Yes bottom balancing has been replaced with top balancing. Bottom balance was from the days before BMSs were put on the battery. Top balance is a more practical method as it happens when power is available vs near shut down.