He has stock controls and an overboost condition. You eliminate questionable stock controls for troubleshooting reasons.
Plus, your 'multiple factory orifice size' thing is not quite correct. When GM reissued the 'factory' Y for sale, their new (most likely overseas) supplier messed up and made the orifice size the wrong size. That wasn't for tuning reasons, that was because GM didn't bother to QA their parts and sold them anyways. And on a side note, they were alerted to the problem and didn't care.
You are correct in the fact that all the extra gimmiks can only raise boost above the wastegate's base setting. but a faulty hose, solenoid, wizbang whirlygig, can cause a severe overboost condition by leaking the pressure signal before it gets to the wastegate diaphram. That's why the OP needs to take every one of those out of the loop and re-introduce them one at a time to figure out what the offending character is.