Question about Transparent Objects in MHX2

[MTKnife]

When I import a Collada or Wavefront file into Blender, I have to add a bunch of transparency settings to the eyes, hair, eyebrows, and eyelashes in order to get them to display properly--starting with setting the objects in question transparent, and finishing with the materials and textures.

When I import an MHX2 file, the material and texture settings are already present, but I still have to enable transparencies on the objects themselves.

However, when I select "Merge Body Parts", combining these objects with the main (body) object, I don't have to change anything: the body is not transparent (and setting it transparent can cause problems, if parts of it are beneath a transparent piece of clothing), but, as far as I can tell, the eyelashes and hair are displayed and rendered correctly. Does the non-transparency make a difference? For the human model itself, I would guess not (the various materials and textures can be combined as if some were transparent, even though the object as a whole isn't), but does the merge prevent the proper effects when, for example, looking through a model's hair at another object behind it?