If your tune is not totally jacked you should pass emissions. Tunes generally look for stock drive ability at partial throttle and more power at wide open throttle.
The only thing done to a tune at part throttle is to compensate for any changes in the sensor maps for parts that have been replaced (eg. MAF, O2, TPS, etc). Everything else is done to increase throttle response and bring in more power at max throttle. Emissions are NOT tested at max throttle, so the major changes in a tune never comes into play during emissions testing.
2012 Mustang GT, Brembo Pkg, Yellow Blaze Metallic