How do you standalone ECU guys pass OBD2 inspection?

[Chair]

I was thinking about this the other day and some searching returned nothing, but I apologize if this has been gone over. I get how a parallel setup can pass the scanner, but what about plug and play systems? The only thing I could think of is to unplug the stand alone and plug back in the OEM ECU a day before, but still that'd only work for those whose stock ECUs can still handle their car. Fueling mods and FI would make that impossible.