I'm going to go against the grain. Before dismissing me as a knucklehead, hear me out.
I've been a Clickbank merchant, affiliate, and customer. As a merchant, I provided a 50% commission to those who made the effort to sell my products. And I gave them plenty of tools to do so. When a customer purchased my products using his affiliate code (without asking me), I expected that customer to generate additional sales. If that didn't happen, it affected my view of that customer.
In addition to the product, customers had full access to me. That wasn't a part of the package; it's just how I personally enjoy conducting business. If they had questions, I made myself available. If they needed advice or guidance, I was there. However, if a customer purchased my products with their affiliate code and then failed to generate additional sales, I made myself less available to them.
The reason was a matter of respect. I felt they were undercutting, for their own convenience, the price that I had set for my products.
As an aside, many customers approached me and asked, "Hey, would you mind if I purchased your product through my affiliate code?" I always welcomed them to do so. Further, many customers purchased my products for the full price and went on to generate affiliate sales. Whenever I was able to track them down, I'd refund their purchase with a personal email thanking them for their efforts.
As an affiliate, I've approached CB merchants and said, "Hey, I've generated 10 affiliate sales. Here's my affiliate code so you can verify that it's true. Can I get access to your product? That way, I can sell it more effectively."
They have always complied. Again, it's a matter of respect.
Regarding whether CB actually allows customers to use their affiliate code to purchase products, understand that CB has a vested interest in every sale. In my mind, that reduces their credibility (in this matter, at least).
Is it right? Is it wrong? I dunno. I'm merely offering my perspective. My hope isn't that it sways you to one side or another. Instead, I just wanted to add another slice of insight to the conversation.