In my quest to avoid the export dialog, I wrote a python script that offers the same functionality that merge_visible_layers does but also removes the non-visible layers.

The script only uses one pdb call, which I thought was really cool and perhaps meant that it would be easy to add a toggle to the existing merge_visible_layers dialog that would allow discarding the non-visible layers.  The one pdb call makes the script really work as a one step before saving as a transparent png.

Here is the relevant portion of the script:

    for layer in image.layers:
        if not layer.visible:
            image.remove_layer(layer)
    
    final_layer = image.merge_visible_layers(merge_type)
    if merge_type == EXPAND_AS_NECESSARY:
        pdb.gimp_image_resize_to_layers(image)

I will attach the script in case anyone wants to try it.