Its not the explosion that deals damage in this trick, its the fact that the rock spawns on you and the game detects that you're out of bounds and insta-kills you. The final shot is likely done while clipping slightly into the seem between the two rocks in the top right corner, keeping samus just high enough not to be out of bounds.

I can get this version of the E.M.M.I skip maybe 20-30% of the time by intentionally trying to shoot while jumping in the very top corner between the rocks. I wouldn't say its worth it though with the original version not being much more difficult, and having a 100% chance not to kill you.