This is the truth. 
Remember? They couldn't kill one and other - but he was going on about how he would find a loop hole and kill him...? 
Then, right before Ben killed Jacob he said "so you found your loophole" 
Basically he somehow became an image of Locke or whatever... used that to convince Ben to kill Jacob, due to the fact Ben was threatened and intrigued by Locke at the same time... 
As for the bottom of the sea shit, the plane landing in LA, yet having everyone on board - but with opposite stories (Hurley having good luck, boon (name check?) not being with his sister.. etc... and wut ?! Desmond on the plane..... well that my friends, is just frickin mental crazy sh*t...