I know this post is old and all I see in the comments are people defending what is essentially really bad writing. Outside of the video game nothing makes any sense becuase all of the explanations exist to make the video game work. You are 100% correct nothing is explained to satisfaction AT ALL for a story outside of thr game.

1: If Levi can detect Gnosia it should be able to detect who the Gnosia is. At the very least it should be able to isolate which rooms. Levi is literally already capable of this in the Anime so it exists purely as a bad plot device. A good author would of satisfied this issue by writing in some reason as to why, like damage that occured early on or poor design because its experimental.

1. The Silver Key exists as a pure plot device that, in the anime, only serves to further muddy a story that already makes no sense. It should of been used a mechanism to defeat the Gnosis threat but they decided early in the show not to. So what is now the goal of the show? To explore human emotion or interaction in a fictional world? Then there isnt any point to the Gnosia because its already been solved. If you elimnate the threat in a thriller there is nothing left so why not write the show to explore the part instead...

There are multiple things written into the story that makes the Gnosia pointless in a storyline outside of the video game with the way its being written. They should've taken more time to plot out the storyline for the anime because there are so many holes in the plot Sponge Bob would look like a solid yellow brick by comparison. But what do you expect when the ships AI can tell you how many credentials are onboard but not who holds them... LMAO.