Warranty and after market parts

So, my Tundra is a couple months old, and like everyone else, I have been putting together a wish list of upgrades I'd like to do to the truck. I've already done a few practical cosmetic upgrades: drawers, topper, bedrack, but am also interested in eventually doing additional work that I am concerned may impact my warranty like a lift or second battery.

The Toyota warranty states
"Alteration or tampering, including installation of non-Genuine Toyota Accessories" and
"Installation of non-Genuine Toyota Parts" are not covered. I understand that to mean that in addition to the items installed not being covered, any altering or tampering to the truck may void the warranty completely.

Has anyone had an issue filing a warranty claim due to aftermarket add-ons? I figured someone here could help clarify.

Thanks all...