They can. It's all just bits. If your files don't and your API does, it is simply because your files don't and your API does, not because files can't and APIs can. Files can have metadata and APIs can be written that treat things as blobs.
There is a distinction, but it's not API vs. file, it's what semantic context you're in. Your MP3 player reads out the ID3 tags, because it's in a music player context. Your backing cloud store (like Dropbox) just sees blobs. Interoperability is less about agreeing on file formats than agreeing on semantic contexts. (Yes, file formats are important but they come later, and most arguments about them are actually arguments about semantic contexts.)