What exactly did you use to program the ECM? I see Hypertech has an issue "TPMS CONTROL: This feature allows you to turn the Tire Pressure Monitoring
System (TPMS) off and on. For those of you that have non-factory rims, this
means no more warning tones on startup and no more TPMS warning light.
There is a slight downside – DTC B2204 (ECU Configuration Mismatch) from the
Wireless Control Module. It doesn’t set the Check Engine Light, but it will be
there every time you read the DTCs.".
What changes are there besides the engine tuning parameters for the supercharger? It may be set now and you have no control to get rid of it with the supercharger configuration and or was just an added feature which you can change. You need to find out what all was changed then either work out from there or you may have to live with it. Get this resolved first then work on the other error code.
Break down of the C0460 for your info is C=chasis, 0=SAE, 4=Auxilliary Emissions Control, the 4th and 5th characters are the specific fault codes that point to a module and or sensor. I can't find this list but will respond back if I do.