Just thought I'd share my experience as I could not find a situation exactly like mine. In the end it was no big deal, but seeing ECU Tampering as the failure reason did cause me some stress!
2013 Evo with intake, down pipe, stock cat, and exhaust. Cobb tune on ECU.
Failed Emissions on first go for "ECU Tampering" - Got sent to the Waiver Station where they do a whole visual inspection.
De-tuned the car to stage 0, kept out of boost and below 3000rpm to get sensors ready.
Failed 2nd attempt for "Misfire Sensor Unsupported" - It must be disabled because it came back on quick after the next step.
Uninstalled the AP. - The Emissions Readiness function still works which is great. Got the car to have everything but "EVAP" ready by driving around below 3k RPM again. They said they could test it with only one sensor Not Ready.
Took it back in an hour later and passed emissions.

 

They've started catching the misfire monitor being turned off in NV as well. They don't do a visual at the emissions lab though. They just have a computer that does more looking and they're able to tell you the actual "issue". It's easily fixed with open source. Not sure about the cobb.

 

They would not have done a visual if it passed on the first attempt. The basic stations are just OBD II and Gas cap. Fortunately the re tests did not cost more money. Paid only for the first attempt.

 

In NV, the normal emissions/smog check station also don't do a visual on OBD2 cars. I was specifically stating the that three cars I know of that have been flagged and had to go to the DMV's emissions lab did not undergo any visual inspection at the emissions lab either. They just do a little more digging in the ECU to tell you why it's not compliant, and the people working there know a lot more than the regular smog check places, so they can explain what the issue is.

 

Yea they got in and started making sure nothing was spliced near the dongle. They saw some of my hard wire job for my dash cam and radar detector. They really just looked to see if there was a cat on it using a mirror. But I saw them really dig into this old jeep before me making sure it looked safe and sound. They knew the tune was probably messing with it. They were also not surprised when I returned such a short time later. But they also see way more modified cars come though. They popped the hood and looked at the turbo and what not which is all stock. Real quick visual inspection. I can't say how it would go with someone actually modified in the same boat.

 

I don't understand why someone would want to disable the misfire monitor.... If you have a false misfire code- why not just disable that specific code? (for example, p0300?)

 

It's an OTS map. So that would be a question for COBB.