I've found that little light isn't nearly strong enough to illuminate the Met-In box sufficiently to make much of a difference in seeing things in there.
I'd leave the seat up if I were charging. First, because I'd hate to walk up, start up the bike and ride off, forgetting that the charger's plugged in. Second, because I'm not sure how much gas these batteries give off when charged that would build up in the Met-In box.
So, the Met-In box indicator light on the dash would be more like a "you forgot to lock your seat" indicator, rather than a "you forgot to lock your seat, and the Met-In box light's going to drain your battery" indicator.
If you put the cigarette lighter jack below the front of the seat, you'll have heat problems, since the top of the cylinder is right there, and you'll have an extra thing you'll have to disconnect / move out of the way when adjusting the valves or doing any engine work that requires removing that panel under the front of the seat. I can't think of a good alternate location that's protected from the elements, easily accessible, and protected from engine and exhaust heat, though.
I don't use any accessories when I ride, so I wouldn't need it except for charging, but it'd be real handy to be able to just plug into a good samaritan's car's cigarette lighter for a few minutes to get a charge if my battery's flat.