Isn’t that at best a really awkward metaphor?

“This company needs to be transparent. And by that, I mean the company should be visible. But imagine there’s this wall between you and the company that you can’t see through. So, you can’t see the company. Well, that wall should be invisible!”

Kind of odd, I think. Even something like, “We need transparency into the company’s business practices” is a little better but still cumbersome.

You can twist the meaning in three jumps:
1.) “I want to make myself clear.” — To use the communication theory jargon, I want my signal to be clear of noise.
2.) “I want to be crystal clear.” — I want my signal to be as clear of noise as crystal is clear of imperfections.
3.) “I want to be transparent.” — I want to be invisible.

Remember, crystal’s clarity gives it its transparency (i.e., transparency is a function of clarity). They are not synonymous.

Why not just say the word that already means what you think it means?

“The company should make its accounting practices apparent.”

However, while I like your alternate take, in this case I believe that the implication has always been the transparency of the “outer shell” – allowing you to see the inner workings of the matter at hand. Like this model engine – http://www.hobbyplace.com/images/revell/car/rmxs8883.jpg – the outside is “transparent” so you can see the movement of the pistons, rods, etc. to see how the engine works. Meanwhile, your car’s real engine, cloaked in heavy steel, is a magical mystery in the way that it creates propulsion for your car.

Likewise, a company might seek to make its accounting practices “transparent” – meaning that the normally opaque wall of secrecy in how they make their “money-making magic” happen is pulled back; they are now forced to “show their math.” The Wizard’s curtain in Oz has become a transparent shower curtain, and you see all the levers and switches and the little old man behind the microphone.

Just my take – I enjoy the blog!

–Mark