You are correct in thinking that the H&S will negate any changes that the factory makes. When you load an H&S product you get an H&S calibration file. Unfortunately, when we build a file, it is based on a factory file. So if that factory file contains a potential for certain DTCs or any other issues, our tuning file will inherit those same traits. Remember though, this ONLY is speaking of software. There are also updated that the dealer can do that pertains to hardware. I believe there have been some NOX sensor changes and other updates that are replacing hardware on the truck. These changes WILL remain even after tuning with the H&S and might fix your problem.
We currently require multiple trucks to have issues before we attempt at a calibration fix. I don't know that we have ever seen another instance like yours, but I will for sure look into it. If I can see that there is reason to adjust the calibration for your particular diagnostic codes, we will do an update.
Keep us posted on what you intend to do for a solution. Thanks!