I don't think adding a programmer is "emissions tampering" since you're not actually removing any of the emissions components.
Unfortunately it is tampering because you are effectively altering the injection timing and quantity. Both of those affect emissions. The Electronic Control Module, along with the software inside are tuned to meet emissions. Hundreds of hours are spent on engine dynos to fine tune the engines to meet the emissions, performance goals, and also endurance goals.
With that said, NO STATE in the union performs a test that matches what the engine has to pass during before going into production. Some states do have testing, but not to the extent that EPA or CARB does.