It probably is going to be dealer dependent. From reading entries on this forum for the last few years, it appears there are some number of dealerships that would question doing ANYTHING to your FJ; others are more enlightened. My dealer is pretty mod-friendly; when I asked about doing the body-mount chop they made a couple of recommendations as to where I should have it done. It might not hurt to check around at local dealers, so if you ever have a warranty issue, you can take your rig to the "right" dealer. FWIW, I have a few mods, and just turned 75,000 miles and have had zero issues related to any warranty.
I will second the above statement, it IS very dealer dependent this issue. Find a dealer that is not adverse to mods. Just remember that it is really up to the dealer to prove beyond a doubt that the mod(s) you have done are the cause of the problem should you have one. One way I handle my mods is I have another certified, very experienced mechanic do my work that is too expensive to have the dealer do and entails more than I can handle, ( we have done a lot ourselves, but I am no mechanic ) and I keep all receipts. This shows that I am getting my mods done by a competent, known local businessman not by joe blow down the road and that I am having them done in a responsible manner. And don't believe everything dealers tell you either, get second opinions and consults from other mechanics. If you encounter any resistance at a dealership, leave and find another dealer to look at the rig. Those who are uncooperative will give you signs, my advice is to seek help elsewhere when this happens. You have a choice on whom to employ for help, and you are paying for a service, don't feel you ever have to take only what you can get, you paid for a warranty, use it if you have to but be smart. Oh and read, understand and re-read the whole warranty so you know it inside out. Then they can't snow you.