I remember this from childhood and tried to find it several times. Nice story. I think of it often when certain software systems I work on become overly complex.
I read it just now because of this comment and it was a joy! I recently read the history of the mbta book, which helped me understand the old names of lines and stations. The fictional network has a few connecting lines that never existed, but every line they actually ride and every station they visit is (or was) real.
https://en.wikipedia.org/wiki/And_He_Built_a_Crooked_House