I guess I understand somewhat why they’d refuse to test a ‘non stock’ car. But I don’t really see what they accomplish by doing so unless they think someone is going to write custom firmware themselves solely to make the car pass emissions testing. People with that degree of expertise would likely be able to make the version or checksum, or whatever they’re looking for agree with the stock programming anyway.
Anyone who has the equipment to alter their car’s programming (unless it’s been sold, like in this instance) would just put it back to stock for the test, then switch it back to however they wanted it and be on their merry way. I have a tuner for my car and if my state did emissions testing, that’s exactly what I would do. You can change the programming on an ECU in just a few minutes, and I can go from stock to custom programming and back at whim. Mine is not a VW though.
In the OP’s case, I would think that the dealer would be able to reflash the computer easiest of anyone. But if they say no, I guess they either can’t or are unwilling to do so. It may be that their own automated equipment needs to verify the original programming’s integrity first before it will proceed, though dealers should be able to just download the correct programming from whatever corporate resources they have. Possibly the ECU was damaged… who knows.
Maybe a salvage yard ECU is your best option. The silly thing is that once you obtain one, it will likely need to be ‘flashed’ for your particular car anyway.