Or maybe... You know when LeChuck was going to stab the voodoo doll, he was going to send Guybrush to an alternative dimention of eternal pain and suffering, but instead Guybrush just got sent to the next room? Maybe he did get sent to the alternative dimention, he just don't think so, and everything after the first stab is not a part of the "regular" dimention, but the dimention of suffering. Guybrush trapped in a modern age world, knowing he is a pirate, even though everyone else thinks he's just a little boy, with his evil voodoo big brother Chuckie to torture him some more when his parents aren't watching (Guybrush can tell his parents about Chuckie's voodoo powers all he wants, his parents will just think he's fantasizing). It got to be like hell for Guybrush...
If this is the case, LeChuck doesn't need to be Guybrush's brother, since the parent skeletons is just a part of the messed up alternative dimention.
So guybrush basically ends up in another dimension -ours.
What if this famous "ron gilbert approved MI3" was actually supposed to be set in the present world