Desmond has vision of "Not Penny's Boat" after Charlie crashes car into marina

In the car, Desmond and Charlie hear Drive Shaft's hit song "You All Everybody" on the radio. Desmond is not impressed by the song. Charlie then gives Desmond the choice of either getting out of the car or to let Charlie show him what he's been talking out. Charlie then grabs the steering wheel forcing the car into the marina, the same one where Desmond and Penny docked their boat and where he was shot by Ben.

After the car is submerged in the water, Desmond frees himself but Charlie just sits in the passenger seat with his eyes closed. Desmond makes his way through the open window and surfaces, but only takes a few deep breaths before going back for Charlie.

Underwater, Desmond tries to open Charlie's door, but can't get it open. Charlie opens his eyes slowly, turns toward Desmond and places his palm on the glass. Suddenly, in flashes, Desmond sees Charlie from the season three finale "Through the Looking Glass," pressing his hand against the flooding com room of the Looking Glass Station that says "Not Penny's Boat."

After a moment, Desmond snaps to, opens the door and brings Charlie to the surface.

So it seems to have taken a life-altering experience in order to cause Desmond to have a clear vision of the original timeline, much like Charlie's almost dying on the plane which was similar to him being on the brink of death after Ethan hung him from a tree in season one. What does it all mean though?