Nothing you do to your truck will "void" your warranty. Nothing. If you modify your truck, and that modification can be determined, or believed, by the dealer to be a contributing factor to a warranty claim, they will deny the claim. If your dealer is OK with electronic power mods, and will honor engine warranty claims, knowing or believing a power mod has been used, you have a unique dealer. How they are putting this over on GM is curious, as their policy clearly states otherwise. You can't hide it from any competent dealer tech. A replacement PCM, perhaps, but even then not 100%.

If you are using a plugin module and relying on DIC mileage calculations, you may be in for a bit of a surprise, and not a good one. The modules "lie" to the PCM to give you extra power (fuel). Part of that "lie" requires the PCM to "lie" to you about your fuel economy. The modules you are using are not an exception. Driving habits generally determine the degree of variance with the mileage, and will usually be a full swing in the opposite direction of what the DIC indicates. In the end, hand calculation over several (dozens) tankfuls is the only reliable method of economy calculation. However, a completely stock vehicle will be generally accurate. More refined uploader programmers and PCM updates can, and usually do, retain the PCM fuel map accuracy.

2006 began the 100K mile powertrain warranty (actually 2007, retroactive to some 2006 models). Depending on build date, a 2006 build truck may, in fact, be covered by the 100K mile powertrain warranty. The tranny, last I checked, was part of the powertrain. GM has always, since 1978, warrantied Diesel engines for 100K miles. Nothing new there.