depends on how far they look. A tune typically just make the EGR as A Non-Report (NA). Most shops will just look at a pass fail. if they look at the individual systems and they see the EGR as a NA and they know it has an EGR then they may raise a red flag. So it does more than turn off the light, but it does not report a "PASS", rather a Non-Report. I am not sure if Tom's tune is different. But the EGR delete from Focus-Sport, that is what it did. Worked well for a few years until some stuff happened and the state inspections people looked at it and said... "wait a minute..."
2001 ZX3 2.0L Zetec-
Hatch Nation #42
Going through Rebuild See "The TICK Build Thread" for details (http://www.focusfanatics.com/forum/showthread.php?t=289168&referrerid=62897)