Any software that turns off the post-cat o2 sensors will cause an automatic readiness fail and will not pass smog. However, cars that require this would not pass regardless due to the cat checking of the stock emissions programming.
Any car that has software whether its Powerchip, ESS, Evolve, Dinan, etc.. will pass smog as long as this function is left turned on. Stage II software normally has cat delete and they will fail the on-board test although they may past the tailpipe test.
If you have cats which are borderline CEL, you can squeeze by if you avoid prolonged drives on the freeway. This goes for tuned cars and stock cars.