It's also rather unfortunate that the Emperor apparently didn't bother to leave any instructions on how the Throne works or how to repair it, nor (it appears) did he leave any information on any other technology he was working on. It was all abandoned post-Heresy and never restarted. For a far-seeing guy not ensuring that his work continued seems short-sighted. "Hey Dorn, old buddy, before you put me on the throne and never talk to me again here's the password to my computer. All my project notes are there, make sure the good works continue".
There might be huge volumes of notes on how the Golden Throne works as an entrance to the webway
. the Throne was never intended to be a life support machine and by the time it needed to become one, the Big E was hardly in a position to write an instruction manual for it.
That said, there's an equally good chance that he never bothered to compile instructions for lesser men. He was immortal and fully expected to always be around to explain how his gadgets work.
As for keeping an STC locked in the basement...
When you backup your hard drive, do you back it up to DVD, or just a folder on the same drive?
The STCs were scattered across the whole galaxy - that's the perfect backup. It failed, I grant, but the chances of every world in the galaxy loosing, destroying or breaking their STCs were astronomically small. Having one more in Terra wouldn't have helped, since there must have boon others on Terra that were also lost.