and if the CG cert isn't, it becomes some kind of gray zone, whereas the checked box makes it a black and white non-question.

Even if the bulb/fixture is CG approved, there is no telling whether the actual bulb/fixture met specs at the time of an incident. There are a whole lot of variables, such as battery state, installation (length of wire run, wire gage, bad contacts, etc) and age of bulb/fixture. But in the real world of check-boxes and administrative bureaucrats, that's not likely to come up if the box is checked. Any argument becomes limited to whether the light was on or off or visible etc.

If it isn't checked the burden is probably on the boat owner to prove he/she met regulations.

From the little I've read about maritime collision cases, there is usually some division of fault with both parties at least partially at fault, regardless. Attempt to comply or degree to which someone came close to complying does make a difference.