Well, Nintendo's non-in-game descriptions/renderings/histories have always been pretty fluid. Remember how Mario looked on the original Donkey Kong machines? Really, I think it's best not to take anything that isn't inside of a Miyamoto-approved Mario game as offical Mario cannon.
edit: but I actually agree with you, as someone who's also a nostalgia-freak, that there's no need to go changing the instruction booklets/art that go along with classic games. I wouldn't want Nintendo to produce art that featured a modern-looking Mario battling Donkey Kong for a virtual console DK re-release. Or change around the classic Link art from the old Zelda games to better match Wind Waker's stylings.