It's trivial to add an .mp3 (or, as I prefer, .m4a) to iTunes and have it sync to your phone. And that's really the model: files of certain types are handled by certain apps (on the mobile device and the computer, respectively), and sync is handled by those, as well. It makes things very simple, convenient, and consistent, and allows for rich metadata, without having to deal with the filesystem (which is really not good enough for that).
> I'm sure if she only ever used an apple computer with apple's itunes software always running on it,
That's not required. Macs come with iTunes, and on a PC you can install it. An iPhone is not a hard disk, but a computer with its own operating system, and you need dedicated software to communicate with it, imagine that.
> and no one else but her ever used it,
That's not required. You can have multiple accounts on your Mac easily, and you can also share music by putting it into a shared folder and creating respective libraries, which manage the metadata (rating, last heard, etc.) for each user independently.
> and she paid for every piece of media she ever put on her device by using the itunes store
That's not required. Most of my iTunes library is ripped from my old CDs (when iTunes came out, the motto was "Rip. Mix. Burn."). You can trivially add audio in a variety of formats (and if a format is not accepted, transcode it using eg ffmpeg).
> any deviation from that very narrow 100% apple-everything set up
Well, as outlined, it is rather special circumstances that make it cumbersome. The fundamental assumption, though, is that you get media from your computer to your mobile device using dedicated software, and I agree that that's problematic: not so much the "dedicated software" part, I have no beef with that, but you should be able to add an .mp3 or .epub to the respective library on the mobile device directly. I hope Apple addresses that without destroying the ease of use and powerful metadata we have now.