Yes, that makes perfect sense. And even if the position of the secondaries was known by the tuning module, it would be almost impossible to know what the airflow into the engine was when both sets of throttles were at the same percentage of open. For example, if both sets were open 5%, there would be less flow if only one set was open 5% and the other was open more than that. The two sets would actually take turns being dominant (easy boys!) and I think it would be almost impossible to generate a curve that would work very accurately to predict airflow based on the positions of each set of throttle plates. Or put in a shorter version: 'da secondaries gotta' go.
Besides that, if anyone is sophisticated enough to use an auto tuning manual it is not likely that that person would need the secondaries in the bike anyway.
And I don't think it is esoteric, I think it is a fascinating topic, just like other tuning and induction mods. I am reading about the other guy who put a turbo on his C-14 and find it very fascinating. He attacked the problem a bit differently than you did and I am quite curious about any differences in your two executions.
By the way, very glad to see you back. As a small, Polish ferret, do you have an interest in meeting a regular sized, desiccated American squirrel?

Brian
This post is a bit esoteric but important to some of us mad scientist types!
The auto-tune module (great device) uses a connection to the throttle position sensor (TPS) to determine (guess what?), throttle position!
This input tells the PC5/auto tune (AT) how much air is flowing into the combustion chambers. It then determines how much fuel to add according to your AFR settings and what the Lambda sensor is reporting back.
Problem here is that the TPS is not a true and accurate source of how much air (or air/fuel) is actually getting to our hard-working pistons because the secondary throttle plates are the true and most accurate controller of airflow.
The A/T might eventually sort it all out but it seems more likely that it will be a very confused little device trying it's best to screw up the fueling.
My thoughts are pull out the secondary throttle plates before installing and activating the A/T.
Discuss?
Fretka (a small Polish ferret) 