Taking all my experiences in the game and all my runs in the vault together I can only think of one solid conclusion. This came to me as I watched the new TTK video... Where the dude says he won't tell about the secrets in the vault. They set the vault up and it probably had all these extra and hidden stuff in it. Many of which probably include some of your theories. But they took out most of the extra stuff as the game was broken down and split up into the 2 DLCs/ gutted. They left a few things like the extra chest if you kill the Templar with no teleports but most was taken out. I would be willing to bet they add back some of this stuff with TTK so that they can add some interest back into the vault after all the new stuff comes out. Think about it and how bungie has treated us/the game from the start. But who really knows?