When I was talking about the "yucky" marina hose snaking through the accommodations, I meant the dockside water hose. The diesel fill was on deck. (I understand your system too though; if you're mostly filling from a watermaker I can see it would not be as much of a pain as with jerry jugs or marina hoses.)
When I did have water fills on deck they were forward on the side decks and the diesel fill was near the cockpit, so they weren't right next to each other. For me, I'd rather be careful and have them all on deck. But there are trade-offs, and I'm sure others would make the opposite choice. I just wanted to point out a couple of downsides that go along with the choice to put fills below. I know they all have their plusses and minuses.