Most dealers are pretty good about separating the mods from what is faulty. Just keep in mind the warranty allows for pretty much any excuse to not repair something under warranty. So, the interpretation of the warranty can vary greatly from dealer to dealer.
Like something with the transmission, mods to the pipes aren't going to look like the cause of the defect. However, it is feasible to burn out a valve due to incorrect AFR if you put on a FI controller and inadvertently cause your bike to run lean.
Like something with the transmission, mods to the pipes aren't going to look like the cause of the defect. However, it is feasible to burn out a valve due to incorrect AFR if you put on a FI controller and inadvertently cause your bike to run lean.