I've got a reply. At least Limited Run's customer service replies quite quick, I'll have to congratulate them for that.
So their stance is that the artwork appears as intended, just like with the Full Throttle box. I send them a reply, saying that this can't be the case, because LucasArts themselves used a lighter, less contrast-rich design in their original release and multiple re-releases (thanks @Torbjörn Andersson for that argument), but I don't think they'll ever admit that it's a fault on their side.
Well, at least I'll get a replacement mural and poster.