Got the updated software today and I tried it out on the '05 Monte. IT WORKS. The cat diagnostic does not run at all with the new settings (disabled via coolant temp qualifier and maximum number of tests allowed per drive cycle set to 0). The fuel trims work normally and AFRs are right where they are supposed to be (and nothing locks full rich ever like what it was doing). I was also able to disable all rear O2 codes so those would never set either.
I am now working with my tuning software vendor to get these parameters added for all 01-up applications supported.