Bonus update. I'm learning so much today.
In speaking to Matt @ EQT, the tune does lock VCDS out. Cobb uses the same software in 19-21 MY cars so Cobb assigns a new ID that's different from the native, and the native ID is what VCDS would read. If flashing back to stock doesn't restore the native ID (I don't know if it does or doesn't) then VCDS would still not work.
I also don't know if the shop installed an is20 or is38 wastegate, and the calibration procedure is different. Only is38 can be done engine off, is20 would need to be engine on. It could all be done from the Accessport, which might solve the problem if they know how to do that. I believe they are closed now so I might not be able to troubleshoot this with them until tomorrow but this gives me hope.
EDIT: Shop would have to completely uninstall the AP to return it to native ID. If they did anything else it would still lock VCDS out.
Matt also says the tune runs stock voltage on the wastegate circuit. The calibration voltage is a different reading/voltage from what the circuit sees I gather. He believe's they are just trying to calibrate it the wrong way.