It is ironic that the only difference between your design and the PE's (adopted) design was the signature. However, from the regulator's point of view (the EPA in this case) there was an important difference: there is a documented record of the PE's competence and there is none of yours. Whether you are in fact fully capable of doing the design is not the issue.
It's not about giving proper credit to each and every competent engineer. It's about having a fully documented paper trail so that if the design is ever called into question by anyone, the regulator will be off the hook. They aren't willing to take your word for your competence, even though you proved it to be more than enough to do the job.
You feel it wasn't worth the money and that may be true in the objective sense. However, the PE had to do due diligence in reviewing the design, and while that is easier than starting from scratch, he did have the hours in to do that and of course he now has the liability for it for years to come. So he or she did earn the fee.