An isolated DC-DC charger has one negative connection for each battery and there is no internal connection between the negatives. They are required for systems that need to be isolated which could be for a number of reasons including;
Limiting corrosion (Typically marine applications).
Preventing noise on one battery system from effecting the other battery system.
For systems that do not require isolation, either unit can be used, however the non-isolated unit is cheaper and requires one less wire to be installed.
In automotive systems, the negative of both batteries is typically connected to the chassis of the vehicle. This is a non-isolated system, therefore either unit will be suitable.
Caravan, RV and 4X4 customers tend to purchase to Non-Isolated Victron DC to DC chargers with the most popular being the 30A 12/12 DC to DC charger.