
@ Bagheera : I admit that my initial assumption was that the seal only blocked the main shaft, and that for HIP, SEELE needed two spears, so when EVA-13 was completed Kaworu didn't bothered to jump outside the inverted pyramid and preferred to take the long and relaxing route since they can break the seal now.
But Fuyutsuki's dialog when everything was over and the fact SEELE intended to use Mark.06 (a single entry plug Eva) 14 years ago implied that they only needed one LoL for HIP and that the added LoC was only part of Kaworu's plan.
But TMB's theory that the seal encompass all of Lilith's Chamber is far more likely.
@ Freaky : nowhere its implied that Gendo was the one who ordered Lilith's Chamber to be sealed. Gendo knew that Misato would try anything to stop the impending Impact, even a last ditch desperate assault, and he counted on it : since he modified the LoC, he knew that Kaworu would try to abort the operation, and he made sure that Shinji was too broken to listen to his copilot and will grab the spears nonetheless, leaving to Kaworu only one option to stop 4I : killing himself. WILLE will then just have to finish the job by extracting Shinji from the weakened EVA-13.
Had Kaworu not decided to kill himself, WILLE would had been completely impotent to stop 4I, all of Gendo's plan hinged on Shinji being too insane and desperate to fold it and Kaworu loving Shinji too much to not kill himself to weaken EVA-13 and let WILLE finish the job.
And in the end Keikaku Doori.

We always wondered just how good of a planner and manipulator Gendo could be, and 3.0 gave us that, this is Gendo at his apex, the man who fooled and made dance with strings absolutely everyone, even the millenia old immortal monoliths!