ALAC is open source and you can feel free to contribute to it or "adopt"/use it.Apple has been using ALAC for a long time on difference devices and platform. Moreover, according to Wikipedia, "compared to some other formats, it is not as difficult to decode, making it practical for a limited-power device, such as older iOS devices". "Adoption" is not a reason, from my point of view, ask a company/app abandon an open sourced format to use another one.

That seems to imply that there should only ever be one format for any particular application.

Because iTunes doesn't support FLAC.