No in-story explanation is given on how Atrus constructed the whole installation and the rails for the maze, nor for why he took the trouble to do it.
Mazerunner was designed by Chuck Carter. He was inspired for its shape from a "puff fish" (possibly Flounder) from "The Little Mermaid" his daughter was watching.
The design differs between original Myst and realMyst. In realMyst, the vehicle is more elongated, it bears a wider viewport in the front, has metal flooring instead of tile, and it is open from front to rear.