I'll be the first to admit that CAIs sound pretty sweet, especially at full chat. The argument as to whether they add any kind off significant performance gains to these trucks has been hashed out on these forums many, many times. I personally don't see any kind of improvement over the stock intake setup with them, at least not on the newer rangers. The stock air filter is in a hermetically sealed high density plastic box (which, as Wicked_Sludge has pointed out, is much more resistant to heat-soak than metal) that gets a nice, cold feed of air from behind the headlight. So far as I'm aware, there aren't any intake silencers or any other air restrictions inside the intake ducting, but I may be wrong on this point. I simply can't think of where any power would be lost on the stock intake setup. Besides, an engine can only "suck" a certain amount of air: you can't force an engine to take in more air by simply adding a bigger filter. Forced induction opens a whole new can of worms on this subject, but that's for another thread.
You raise a good question about the downloadable programmers. I'm pretty sure using one wouldn't void your warranty so long as you save to OE files and re-flash them before turning the truck in. Might want to check with the manufacturer of the programmer on that one. You could probably find that info on the Diablosport site as they have a ton of stuff on there