This is really the thing right here. I've had to pass emissions testing in a LOT of different places. Some are better/easier than others.
I can say this about the places that I've been that actually look for error codes:
If you have say, a 1989 Mustang that came OEM with an A9L and they are required to check for codes, it will fail emissions based solely on the fact that you do not have the test port that came equipped on your car. In many cases, one would not even pass the visual inspection. End of story.
If the OP thinks that the emissions control people are going to sit back with a cigarette and chatter about the marvelous job that was done to put an OBD2 computer into and OBD1 car, then he is sadly mistaken. Most of these clowns are not even car people. They look at a screen or a book. Their procedure tells them to take emissions accessory 21b and insert into slot 16f. If 21b doesn't fit 16f or if 16f is relocated or doesn't exist... FAIL. They don't take the time to discover the why or how... It's not their problem. What is supposed to be on the car is NOT and that's enough for them to fail you and move on to the next one before the lunch break begins.
If you have the same car in a state/county that DOESN'T check for error codes but has a dyno, idle, or high idle sniffer test then the only thing that matters is what is coming out of the tail pipe. OBD2 vs. OBD1 makes ZERO difference in this case. The same adjustments to emissions control methods can be made with EITHER of these setups using the same methods but different equipment. EITHER of these ECUs can be tuned so it makes no sense to me why anyone would retro fit.
If things like what the OP is talking about in this thread were true, then we'd all be ditching the factory catalytic converters and smog pumps in favor of 3-way catalytic converters. They're more efficient and reduce emissions more than the factory pieces. Why don't we? Because that's not how they operate. They want the factory equipment or the car fails, REGARDLESS of the fact that the OEM converters are inferior.
The best way to pass emissions is and always has been, to have on the car what CAME on the car and to ensure that it is all in good working order.
I hope I get a tester who is not a car person that will plug into the diagnostic port see no codes and send me on my way. Only going Odb2 because the car year is 1998.