The default tile sets supplied with RPG maker display horizontal planes as seen from above and vertical planes as seen from the front. Traditionally with the orthographic projection in 2D computer games maps are designed in a way that players will descend hills/staircases from the top of the screen to the bottom, and ascend them from the bottom to the top.
If you were to show the traditional perspective (as i described in my sentence above) and the perspective you suggested (in your picture above) in the same map, where the staircase goes downward from the bottom of the screen to the top, you would create a conflict. This would materialise in the vertical plane on the staircases. As this is what creates the illusion of height, or depth in the image. Only one of the staircases would be able to display the horizontal plane and the other would therefore appear 'blank' in the tile (due to repetition of horizontal plane with no vertical plane to distinguish).
It is possible to flip the perspective from top-down to bottom-top as long as you are consistent throughout that map. But in doing so you will effectively 'lose' detail as tiles will be hidden behind the environment, hence the reason 'RPG maker displays horizontal planes as seen from above and vertical planes as seen from the front'.
