The D4 will not allow the battery to run low.
It may reduce alternator output for short periods however it monitors the vehicles battery during this time and will override if the battery is getting lower.
When you start the vehicle the batteries link and provide a load (demand). If the linked (parallel) battery is below system voltage then the system will up the alternator output to meet the batteries demand and bring the batteries quickly up to its expected level.
Luckily there's another factor in battery charging - temperature.. A battery when charging accepts more current as temperatures rise... At this point a slightly lower voltage is better suited to bringing the battery safely up to charge.

