First, modification of any part of the bike can void the warranty for that part and any part it impacts. Notice I said can. There exists a requirement under federal warranty law for the warrantor to prove that your modification actually did, or could be reasonably assumed to have, cause the failure in question. Does that mean Harley won't try to jerk you around? Absolutely not, they've been known to jerk folks around on warranty when there was no modification involved at all. They tend to be famous for it.
Implying that a dealer will cover the warranty as long as you buy all the parts from him and pay him for all the labor is something you hear in a lot of places. Believe it at your own peril. Unless it's in writing from the dealer principle or his legal designee, it's just talk. I find it to be akin to extortion when they imply they will void your warranty if you buy a TTS or Power Commander, but they will look the other way if you buy a SEPST from them. I would never buy anything from folks that use such methods, but to each his own.
As for the subject of the thread, I would definitely recommend something like the TTS over the Fuel Pak and Throttle Pak. The TTS will do everything those two devices will do and much, much more. And if you are worried about warranty, with the TTS you can easily put the ECM back to stock before you drop it off for warranty work. That isn't possible with the SEPST.
Jerry