We've received and checked over the images you've provided. Basically, A5 sheets are by design, 256x512. The reason why you're not seeing those transparent tiles is because those were added in as a bonus, where users can elect to use them as D or E and manually apply em onto the map through the layer feature of MZ. They were not designed to work straight off of A5.
We suggest the following:
For the tiles in the "A5" row, to make usage of the transparent features of rocks and cliffs, put a duplicate of the set in the "C" tab of your tileset onwards.