Aside from hardware compatibility with an actual FDS drive, would it break anything? I would imagine most flashcarts and emulators would only take issue with images that exceed 1MB, like some do with certain hacks like the SMB3 All-Stars hack. In fact when it comes to FDS hacks, I'm amazed that we have yet to see hacks that forgo disk swapping for direct loading of the 2nd bank and hacks that reduce the loading delay to nothing.