Sir, once you tune your car, the driveline warranty is gone(motor, trans, rearend). If you were to throw a piston through the block, they connect your computer to theirs and can quickly see if it has been tuned even if you return it to stock. On the other hand, as long as you have a knowledgeable, awesome tuner, your chances of that happening are al,ost nil. Always run great gasoline and do not get it tuned on the edge. Also, not all of the car's warranty is void. If you alternator or starter give out, that will be covered as your AC will also. Have fun man. Beautiful car!! I own a 2020 Shelby GT500 all stock except a JLT CAI. Someday I will do the exact same mods as you. Again, congrats and I wish you and your family the best!!!
There is a fine line when tuning. I had the tune shop that is affiliated with the Ford dealership tune the car. So if anything happens with the car, they would be doing the work and get it covered under warranty.