Is the modification minor? Yes, it added preload, so it changed where ride height is, it did not add additional travel nor shift the travel (like a leveling kit/spacer on top of the coilover). The cv axle may not have even spun very much unless you run around in 4 auto or 4x4 much. So there is a chance that the leak is not caused by the preload collar. The leak could have been created during the install though. Say, for instance, if they didn’t take the axle nut off and could have over extended it/tore it. Have you checked to see what is actually going on yet?
Should it be covered by warranty given the above? In my opinion, no, whether or not the mod caused it, you can be certain, so benefit of doubt isn’t there. I certainly wouldn’t take a mod off and take it in to try and get it covered, tune would be excluded to that, but that is due the chance that the dealer might flash the truck while it is there.
For fun, let’s set aside the ethics for a minute and discuss some details.
If you were to remove the mod, you are either:
A- paying someone to remove it, possibly align it, hoping to get an axle covered on warranty, then presumably paying someone to redo it all again. The axle is $250, how much is labor to take care of that??
B- you are doing it yourself. In that case just pull the axle, repack the inner joint and put a new boot on it. Or just install a new axle assembly.
that is my 2 cents