In finish construction you can do anything you want to. It's your house and I have seen some interesting things over the years.
Usually the molding is put in and the tile is cut to fit the molding.
As you have pointed out there is a difference in the thickness of the tile versus the plain wall. This will cause you lots of headaches since it not only affects the molding at the tile transition but it will affect the reveal on the door frame.
My take would be to remove the tile, put the molding in and then cut the tile to fit up against the molding.
My idea of a perfect day: No where to go and all day to get there.