I suspect that whoever rigged the engine made a boo boo. The battery isolator should be just that, an isolator. The only thing that normally bypasses the isolator is the bilge pump. I have a DF140, which I rigged, when the isolator is off, the boat is dead, apart from the aforementioned bilge pump.
Re. Connecting the engine to your NMEA2000 network, good luck[emoji849]. The Suzuki implementation of NMEA 2000 is abysmal. You will need an engine interface of a similar era to your engine. They (Suzuki) have changed the hardware & software that make up the interface over the years with each iteration of the engine. Older engines are incompatible with newer interfaces. You used to be able to flash the interface with the software appropriate to the engine year, the current interface can’t be flashed backwards.
The Suzuki outboard owners forum is a great source of knowledge. The member Moonlighter has written a paper on the subject which is a good starting point.
https://www.suzukioutboardforum.com/...a2000-networks