The alt timeline will probably have some sort of significance that we aren't aware of just yet.

I think it would be interesting if Sayid came back as Jacob which would sort of answer what happened to Christian Shepherd. Cas that would mean Jacob can literally possess the dead while MiB can only assume their form.

When MiB referred to his home he could be referring to the alt timeline (rather should be called Another World like in Chrono Cross).

So apparantly John Lennon is alive on this island.