Well the way I see it that sealing jitsu the 3rd used only works on mortals. I don't think it would have worked on Kyuubi since it is a demon, technically a non-mortal, supernatural entity.

My guess is the 4th had a variation of the jitsu knowing this, and used his own life to seal Kyuubi inside of Naruto. Simply because you can't kill a demon like Kyuubi that way but it CAN be contained in a vessel of some kind...

*Edit*


Potential Spoiler





























Also I don't think the 4th was sealed within Naruto. That would mean he technically wouldn't be dead in the traditional sense. And that would also mean Orchomaru wouldn't have been able to resurrect him as he had the 1st and 2nd, and it did show there was a third coffin the 3rd stopped.