I don't see a problem here.
Reflashed ECU can report whatever it wants to whatever query. I.e. hardcoded response.
Unless there is some ROM area on the ECU which handles this function...
Edit: If the ROM part is true we're screwed. If not, then only folks that just change the mapping values would have a problem. People with the smarts to edit the ECU program code itself, can code around it.
Edit again: unless of course the ODB-2 standard includes commands for reading the ECU code/data area contents.... this seems unlikely, and if it was the case, then they wouldn't need to require the cars to support all this CVN/CIN stuff. Manuf would just supply code checksums to the emissions folks.