Every polygon will blend with what's below and if polygons are overlapping the overlaps will get darker. Assuming what you say is correct, that there is absolutely no way to do the models without overlapping polygons, there is no way to do this with alpha.
There are ways to achieve what you are trying to do however. A trick I've used (plus it is used extensively in most dynamic shadow systems, including sswift's) is a multiple render pass technique in which you render the object alone and use that rendering as a sprite. If you don't flip after the render of the object alone the player will never see that render. To get the object uniform in color you set it to fullbright, strip off the texture, and then use EntityColor. Meanwhile set the clearscreen color to white (assuming multiply blending) so that the background of the sprite becomes transparent when you apply blending to it.
There are ways to achieve what you are trying to do however. A trick I've used (plus it is used extensively in most dynamic shadow systems, including sswift's) is a multiple render pass technique in which you render the object alone and use that rendering as a sprite. If you don't flip after the render of the object alone the player will never see that render. To get the object uniform in color you set it to fullbright, strip off the texture, and then use EntityColor. Meanwhile set the clearscreen color to white (assuming multiply blending) so that the background of the sprite becomes transparent when you apply blending to it.