No manufacturer can provide protection for all fault circumstances that may occur outside their control. That said, you were basically given a line of bullshit IMO as a way to open the door on declining any sort or warranty claim. Does it happen - sure but it's pretty rare.
Should modern electronics be provided a separate source of power independent of the CHARGING system? Not in my opinion. Is every boat that does longer passages supposed to swap out batteries as required so they can be recharged? Bloody ridiculous statement really and if they are that sensitive, the manual should state that installation of a power conditioning device is required at a minimum. Should they be run off a power source independent of the STARTING system? This is a completely different kettle of fish to which I am thinking more along the lines of yes these days. Some breeds of equipment are becoming a lot less tolerant to voltage drop created by starting. It doesn't normally do damage but the potential is there.