Actually, it looks like your charger IS ignition protected
Yes, we agree.Within the ignition-protected charger there is a terminal strip where the wiring connects.
The way Sea Ray puts AC junction boxes in the bilge is to crimp the two wires together and have strain relief/cord pull connections where the cable exits/enters the junction box. If the junction box is below a certain level in the bilge, it is supposed to be water tight but I don't recall that level off the top of my head. You probably already have an AC junction box in your bilge for your Air Conditioner system so look at that as a guide.
The 330DA has a junction box on the bulkhead in the engine room near the air conditioning system's raw water pump. Follow the raw water pump's wire back from the pump and you'll find the box. Pop the cover and do what Sea Ray did. A perfect example.
There it is, again...The sand-colored box in the lower right corner is a factory-installed AC junction box.