Basically, you just agreed to settle and not continue to press your valid claims of potential affiliate fraud.
What would have been a better course of action?
Even under the most optimistic estimates, they owed me less than $500. I don't have access to their sales data, so I don't have hard proof that they're committing fraud. The company's legal team could just turn around and say, "Oh, our rep was mistaken when they said we're not following our own policy. We actually do pay according to our published agreement, but you didn't make any sales during that time period."
I could have pursued options for some sort of class action lawsuit with subpoenas for their sales data, but that's a much bigger time and financial commitment than I wanted to put in.