Found the actual game designer. Do you follow Ceave Gaming on Youtube by any chance? If not, you should check out his Mario Maker videos.
I definitely agree with you on this one. In terms of less visible things that would make all the difference in the world for creative potential, this is it. I'd appreciate a few more sub layers as well.
Yep more sub layers would be very nice with the ability to carbon copy basic layout and affect elements in other layers for more intricate puzzle design. I loved making puzzle based levels and one of my favorite included between a past and present version of a level like in skyward sword.
Another problem I had is that moveable elements disappeared when getting out of range. I had to design my puzzle chambers in such a way that the player couldn't move too far to the right or left before finishing the puzzle, otherwise critical elements would de-spawn. One of my levels had you guide a cannon through the entire level which caused major headaches as it would disappear if I allowed the player to get too far ahead or behind of it.