This is just one more of the many questions that cannot be answered with a definite yes or no. Especially with Harley, everything "depends". If you go strictly by the book, then any modification to the engine management system will void the powertrain warranty, as well as be illegal emission system tampering. Funny how Harley gets away with selling those SEPST's and other non-street legal products to consumers to defeat the emissions systems.
In reality, it all depends on what kind of failure you have, whether your dealership service department is run by a by-the-book person, and whether or not H-D itself insists on inspecting the bike prior to approving any warranty repairs. And with a SEPST, they don't have to even visit the dealership to inspect the bike. All they have to do is have the dealership connect the ECM to the computer and H-D can determine if an SEPST has ever been used on the bike.
You're correct in saying that probably the majority of Harley's on the road have some sort of tuning system or device as well as non-standard exhaust systems, and many have had failures and the warranty was honored. But that doesn't mean everyone has that same experience.
Jerry