The files used are actually Ford files. The 17+ APIM is fully capable of running 3.4, but they changed the allocated memory sizes to accommodate the newer version, so the internal storage has to be reformatted to accept the new files. Ford doesn't want to have a bunch of failed updates to deal with if the reformat glitches. They will not be updating our units to 3.4. Cyanlabs figured out a way to do it reasonably safely. I've done two. My '16 Explorer (bought a 3.0 APIM and installed it) and my '17 F-250. Both worked fine.
As far as warranty, I probably wouldn't try to do a warranty claim on the APIM, but I see no reason it would void the warranty on any other system. Magnuson-Moss should be all you need to say if they were to try an deny a claim. The only thing affected by the update is the APIM and with the exception of the reformat, it's all FoMoCo files.