This is my first theory and not all my work.
The alt time has become the big mystery of the show. It has become clear to me that it is showing the lives of the losties without the involvement of Jacob. Their lives are slightly different, they all (so far) seem happier. This has made me think why no Jacob in this timeline ?
The answer could be because he is dead. Maybe some kind of loop is happening. (Stephen Kings Dark Tower !)
The Jacob line to MIB sat on the beach ,"It only ends once, everything else is progress" - this suggests a loop of some kind.
The alt-time line is the next version of the loop. No Jacob and no island. Why ? Because he is dead and the island is underwater !
The finale of Lost will involve some massive struggle between the 2 sides. People will die. Jack will kill the MIB and the island, for some reason, will sink to the bottom of the ocean. An unhappy ending we think ! No !, we will next see the alt time line and understand that the actions on the island of Jack and co will break the loop and reset time. We will see the happy lives of all the losties in the alt time line and realize that this is the real time line from now on.
I think this could happen but I'm not sure I really like it to be honest !