I'll need a save file for testing, but from what I'm seeing so far, transparency only contributes to visibility, not exposure. You may want to be more particular in what part of the game is not mentioning the clothing transparency.
In the game, there are three kinds of states to genitals when it comes to clothing: Covered, Visible and Exposed. Exposed genitals means that they are not necessarily clothed and can be access in the open air. Visible genitals are just being able to be seen--so all exposed genitals are visible, but not all visible genitals are exposed. Things that contribute to visibility of genitals include being exposed as well as tight (body conforming) and transparent articles of clothing. Tight clothing can straddle the line between being considered exposed or not depending on how strict the check for it is (context matters). Transparent clothing doesn't have that feature, so the genitals will be considered clothed, but visible. Covered genitals are clothed and not visible, of course.
Hope this helps clarify.