At the moment the Synth only supports rectangular grids, and there is indeed a rather limited number of ways to distribute a grid of 12x5 pads into 3 rectangles (or less) without laving any blank spaces. That number becomes smaller when you eliminate functionally identical duplicates.
I have no clue how the ep133 maps pads to notes, and the manual does not explain that either, but at the moment the Synth only supports rectangular grids where pads are ordered on row from left to right and bottom to top.
So you can’t map note numbers to pads, you map scales to rectangles, and that might or might not work with your usecase.
If you read the thread, there was an editor, and people did not use it.