I feel like each security level (other than level 1) should be a category of its own? And also why is endroom% a thing when that (I would assume) is the same as beating the game, so it’s pretty much the same as any%?

You can get to endroom at lvl 0 if you can amass the arms to do so. There's no mission elements to mark it but the room is accessible. You have to cheese your way through the main gate however.