Well, I found my old laptop with TIS 2000 and it still works, and I downloaded the file you mentioned in your linked thread and it has a full VIN in it, and according to TIS, the VIN appears to be correct for a ZF6 truck, so flashing an ECM isn't a problem. It's been a while since I've played with an AutoCal, so I'm not sure if they can flash unsecured files, or if they can ONLY flash files that are linked to the same V2 that the AutoCal is linked to.
The only problem I could see would be if your truck originally had an Allison, if we flashed a ZF calibration into your ECM and made sure the ECM also had your trucks actual VIN after flashing the ZF6 calibration, while that calibration would be correct for a ZF6 truck and the VIN in it would match your truck, the calibration wouldn't match what is 'supposed' to be in your truck based on its VIN, so they may still whine. If I'm not mistaken, Cali takes the VIN of the truck and compares the calibrations it reads from the ECM to a database of calibrations that are valid for that VIN, so a ZF6 calibration in a truck that originally had an Allison might not match up with what they say it should have. I could be wrong about that last part though.
What's the actual problem with smogging it? Is it still running a calibration that's expecting an Allison and is throwing a check engine light because of it?