Random question...
How the hell would they know if you had a tune anyway?
The timing advance, change to injector settings, or whatever these tuners do would require the test facility to have all the "stock" programming info for every single year for every make and model of car sold in Merica....
About the only thing they could do is check a CRC, and I still think thats waaaaaay to complicated.
Or are there people at the inspection station scanning through your ECU watching it like its the matrix???
As stated in earlier posts, most states, not sure about ALL, do the emissions tests through the OBD II port under the dash.
Here in MO, state licensed safety inspectors and mechanical repair shops have the option to do emissions inspections. The inspector has to take a test through the Highway Patrol to become emissions qualified.
As far as your question about failing tuned vehicles. The inspector has no control over failing or passing vehicles. He plugs a computer with special software built into it to the OBD II port and lets the vehicle idle for a certain amount of time. If the vehicle picks up any DTCs or the readiness monitors are not set it will fail. The only thing about the test that the inspector has control over is at the beginning it asks if the MIL works with KOEO and KOER. The inspector selects YES or NO. On some tuned vehicles, there may be codes in the ECU due to the tuner changing certain parameters and other things that could even be transmission related. The programmer will lie to the ECU to keep the MIL off, but the codes can still be stored. I've seen some mustangs, vettes, and other performance cars that have had major engine mods done that required removal and reprogramming of the ECU to compensate for these mods. When this is performed, a lot of times the readiness monitors are set to UNSUPPORTED, which will cause them to fail.