As shown in the picture attached, the white outline of the structure block in save mode (at the bottom right) is not the same as the region covered by the blue cubes (which represent air, and appear when the "Show Invisible Blocks" option is set). The structure block on the top left is in the corner mode - I used it in conjunction with the save structure block to detect a region to save.

The region with the blue boxes is the actual save region by the save structure block. The white outline is fake. Although it is of the correct size, it is in the wrong position.