I've titled more than a handful of vehicles in Kansas and never once had them do any kind of aftertreatment checking. Obviously your situation is quite atypical, but I don't think you will run into a problem.
Worst case, you show up and they tell you they are going to title on motor vin and you fail inspection. I don't think they add that to the system, they just don't do anything with it and tell you to fix it before you bring it back.
I titled my 350Z at the title office in Lawrence and the people were complete herp derps so if you want to find a backwoods office, you don't have to go far.
Good luck.
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