I think we might be reading too much into why Rob specifically got shut down. He is not the first, and will not be the last. I suspect either someone called him in, or just through chance he got hit with a sting, or they started going through the list of diesel shops, starting with "A".
I do think the EPA benefits by keeping the perception of diesels as smelly and smokey, because the general public hates the smell/smoke, which makes it easier to regulate diesels more. But I am not sure I am willing to give the EPA enough credit to be planning far enough ahead to go after "clean" tuners first.
Somewhat off topic, I really wonder if we didn't get the "coal rolling" culture springing up and being dicks to the general public, would the EPA be treating diesel modifications like gas modification? I think there is a lot of pressure from the general public pushing the EPA to crack down on diesels. I've been on the receiving end of a smokeout, or even just behind some Cummins bro blacking out the whole intersection, and it is really annoying to have to wait until you can see the dang lanes again. I can understand their frustration, and why they might start complaining to any agency who will listen.