I just had my 2006 E350 inspected at a NY State inspection station. I thought when going in that as a diesel they wouldn't plug in the OBD2 reader. Anyway they did and I was fearing a fail. My unit has a tune from 5 Star that is suppressing the CEL among other things. I have my EGR deleted (let's not start that conversation), and my tune is very mild. I watched the computer do it's thing and everything came out perfect, no codes! I passed. I understand in NY if you register commercial there is no OBD2 reader required.
What is the official software reading? How could it fly through inspection?
In TX all they do is read codes and last time any codes were deleted/reset. (So you can't just delete codes before inspection), you need 50miles or so since last code deleted. All your changes would require visual inspection, so easy to see why it passed. They don't check if you have oem firmware, that would require a whole new level of diagnostic tool.