If you don't ford anything too deep you will probably be ok. It's an inexpensive and easy mod though.
As far as warranty goes it could depend on where you bought it and the integrity of the service dept. Many dealerships look for any excuse not to honor warranty. I had a heated argument with my service dept over a stripped roof rail bolt I could not remove. They ultimately replaced the roof rail for free. Despite these being off road vehicles, Toyotas definition of offroad may be far tamer than ours.
Enjoy your truck and don't worry about it . These rigs are pretty tough and forgiving.
Of course this forum has an addictive influence causing irrational spending and obsession over aftermarket add ons. I highly recommend transferring your bank accounts to your significant other ASAP. lol