Yes. Once I had to deal with that problem, and ended doing parallax for some tiles.
The thread I read back then about the problem, there was recomended one less effective, but easier to use method.
That is to put invisible event, which activates on player touch. That event will make the player transparent, give him through passability, and walk him up the other side. Then remove the transparency and the through flag from the player. From the other side, similar event will move the player down. In best scenario, the invisible event will be only one, on the ceiling itself, with same as player priority, and set to react properly depending if the player is bellow or above.
Is less effective method, and probably more annoying for the player, but is still some option, if you can't find better solution.