I haven’t tried it myself yet, but the previous owner of the car had an Accessport (which came with the car) and several dizzy/stratified tunes in addition to the Cobb tunes that come with it. He simply flashed it back to stock (Cobb Stage 0), drove it until the drive monitors checked out, and took it for CA smog with nothing out of the ordinary.
He immediately flashed it back to one of the aftermarket tunes for the test drive.
As long as you’re on stock, Cobb Stage 0,1 or 2, you shouldn’t have a problem. If you are worried about it, go to the smog shop and pay for a “pre-test” that won’t be reported to the state - they are available to do things like verify smog repairs before going for the “real” test.
The only catch is you pay out of pocket for the pre-test, with no “pass or free retest” guarantees, and then you have to pay for testing again for the real deal.