AqP wrote:I read somewhere that Makehuman gives each item of clothing a responsibility for hiding the skin mesh underneath using an alpha texture. However some applications need to minimize the number of polygons
That information you read is outdated, and was for A7. We no longer use alpha masks, instead we do polygon masking (deleting) now. Which does exactly what you want, for the very same reasons you mentioned.
The "hide faces" checkbox in the clothes library controls this behaviour.
But, same remark as before: you'll have to wait for the new clothes, the current ones don't have a valid face mask for the new basemesh.
AqP wrote:When I looked at the Afro hair in Blender, and set up Blender to display alpha textures (material alpha on and set to 0, texture alpha on and set to 1, not using legacy Blender game render), I discovered that the base layer of the hair is hiding the scalp giving a see-through head. Any comments?
Not immediately, no. I only have limited experience with the different render modes and material settings in Blender, so I often have to experiment a little myself.
A general advice is to set the human mesh to solid (non-transparent) render mode, and the hair mesh to transparency. This should do the trick in realtime. If possible, try controlling the render queue so that the solid human is rendered first, then the hair with alpha (depth writes disabled).