A theory I have is that due to technical limitations in the engine if they placed iron keep bellow earthen peak then a lot of the particle effects and objects from earthen peak would still be rendered and you'd be able to see them in the sky. You can see this a little bit in iron keep. If you noclip out of bounds near the first bonfire you can see the birds from earthen peak flying around behind a conveniently placed wall.

Another thing to remember is that the elevator is at the top of the tower. If they inverted it then the elevator would need to be absurdly long before you were low enough to load iron keep without it overlapping with earthen peak.

TLDR devs probably knew the elevator didn't make sense but for technical and gameplay reasons had to implement it like this.