The EPA sued HD a few years ago and HD paid a huge fine and agreed to be good children from now on. Part of "good kids" is that HD cannot sell a tune module that can change the most important parameters, like A/F ratio; HD also agreed not to delete the catalytic converters ("cats") and only to use EPA-approved fuel maps. HD is required to void the warranty on any bike that has deleted the cats or used a non-EPA fuel map.
It sounds like you got the HD tuner ("Get there tuner and there is in fact a stage 1 map listed for this bike.), so the closest map to your setup w/ FS baffles is the HD Stage 1...and of course, it is blessed by the EPA...therefore it has the EPA-acceptable A/F ratio.
Since the FS baffles flow more than the stock HD, you're right that it's probably too lean -- but that's the requirement to keep your factory warranty. And yes, you're also right that they void the warranty if there is, or was, a non-approved map ever installed. The HD ECU sets a warning flag in the system that alerts the corporate database and the tech that the warranty is void.
Some people decide to say FTW (Warranty) and do what they want, while others have switched the ECU to aftermarket solutions, with the idea to switch back to the stock ECU if warranty work is needed. Otherwise, it's checkmate on the bike.