It's not a glitch, that's just how it works. All three of my 370's did it, and my 2024 Z does it. An increase of 500-700 RPMs every once in a while isn't going to hurt fuel economy in any meaningful way, nor will add any wear and tear on the car.
What car did you have before?
I don't have the TruControl, but I believe the wiring harness plugs into the TMAP sensors, which are connected to the intercoolers. Did you disconnect the battery before doing all of this unplugging and plugging?
Are the free map revisions available if one were to purchase the TruControl thru another vendor, or do you have purchase it directly from the Stillen website for that apply?