Huh. Good to know. But, not a huge deal, really. First of all, California got lazy, and now doesn't require a smog check for the first seven years of new car ownership. So, my 2015 hasn't been smogged yet, and I've been driving on my Cobb Stage 2 tune. When my renewal notice says I need the first smog check, I'll flash it back to stock, and put my stock intake back on. Then, drive around for a few hundred miles so the ECU "forgets" the reflash, and it should pass. After inspection, put the Cobb intake back on and flash back to Stage 2.
It is a problem for someone who has a custom tune and no handheld tuner to go back and forth, or on a car that won't run well on a stock tune.
Also, it's important to put a few hundred miles on the car after flashing back to stock before the inspection. Recently, I had to have my old work van inspected, and did some repairs and cleared some codes right before I took it in. The smog inspector could tell that I had just cleared codes from the ECU, and told me that I needed to put some miles on the car for the computer to forget the reflash. If the testing system flags a recent reflash, it's an automatic fail. Came back a week later and it passed no problem.