Yes it's Koji Kondo's own, or at the very least strictly supervised by him. It's from the official Majora's Mask OST Piano album.
And thing is about the first D is that its effect comes from the crescendo, and the fact that it dies away significantly more after the 4 beats just gives an undesirable effect imo. I dunno maybe if I had a full size concert grand with longer sustain I'd be inclined to think differently but there we go.