I did not check, but I think the problem is that it export the size of the layer, not the visible size on the canvas ➤ before exporting, and after moving the layers, did you right click on each moved layer in the layer stack and selected Layer to image size?
You might want to tell the developer about it, ask it as an option, because the developer might not want that its script change layer sizes without user knowing it (and it might bother other users to see their layer ➤ image changing size), an option layer to image size before exporting could solve things.
Put a link to this thread if you ask the developer
You might want to tell the developer about it, ask it as an option, because the developer might not want that its script change layer sizes without user knowing it (and it might bother other users to see their layer ➤ image changing size), an option layer to image size before exporting could solve things.
Put a link to this thread if you ask the developer
Patrice