Some cars ( SAAB ) marry the radio to the body computer to prevent theft,if the radio is removed it must be divorced then remarried to another body computer. But, the body computer is entirely different than the engine computer.

The 2000 C230 should have Bosch ME 2.0 or ME 2.1 engine control, this is the same as my 97 SL320 / E320 / C280 cars and nothing from the radio is tied in.

MB did tie radios to body computers at some point but I think it was later than 2000.

I'd try to communicate with the engine computer with a scan tool and see if it works. I wonder of the ref station never plugs into the OBD port and just does a tail pipe test. That could explain why it passes there.

What state are you in?