Smog question

So here's the story sorry its a little long,

A friend has a hypertech power programmer on his 03 chevy truck and goes to get it smoged. The station tells him the truck passes the sniffer test but the computer reads a XXXXXX code that says the truck is not stock and so he fails the test. However the programmer is CAL legal and he only basically used it to change for different tire size, read DTC codes.

He has since removed the Tuner and now the CEL is on, total separate issue but maybe related, due to his rear O2's not reading correctly. His computer is not recognizing the O2's for some reason and is taking his truck to get looked at later this week.

BUT


Can anybody tell me if they can truly tell that the computer is not stock?

I wanted to get gears and get a SCT programmer to fix my speedo but now I am afraid too.

Also when I supercharge (when the money supply is up) it with a CAL Legal kit I will change the computer, which On the CARB website they say is OK.

So any help from the CAL guys or anyone would be much appreciated before I invest in my car.

Thanks

What about the other computer adjustments needed it i go the FI route ?

I just want to know if they can really tell or if its BS.