The fact the specs of the iPhone 7 and 7 Plus also now show FLAC support would seem to suggest that it's coming as part of iOS 11, the latest version of Apple's operating system which is due to launch for download on 19th September. Could hi-res audio support be on the horizon too?
Also, it looks like it's a case of one format in and a couple out. Neither WAV or AIFF (which was Apple's own uncompressed format) is listed on the supported formats for the new handsets, or the previous generation.
We've contacted Apple to clarify the situation.