It was just a different style introduced with RMVX and carried on for each version since then, that allowed you to have all your cliff edges on a single layer, and in these particular engines, forced to the lowest layer. It avoided the problem of "what to put behind it" when you didn't know if it might be ground, water, or more cliffs.
I much prefer the RMXP rounded style. You can still do that with VX/Ace/MV by leaving the top of the cliff autotiles empty, drawing in whatever on your map you want to have show behind it (ground, water, more cliffs, trees, etc), and then putting the rounded cliff edges on the B-E tiles and using one of the upper layers to place it. Gets a bit fiddly though, but if that corner bothers you, it'll give you a much nicer effect.