The entire assumed backstory about this is wrong. The narrative was that the album was rejected by the label for being too challenging but in reality Fiona was displeased with the record and opted to shelve it. 

The version that leaked is labeled the "Jon Brion version" but this is also erroneous. He hated the leaked tracks and says they contain parts he didn't actually record. 

\> “There’s music on there that wasn’t even part of \[what I recorded\]. It’s wrong. It’s not like, ‘I don’t quite like the mix.’ I wasn’t happy with \[the leak\] cause I don’t like those versions. It’s stuff that doesn’t reflect what we recorded, for the most part, except for the stuff that’s just her and an orchestra. That’s just right — but as far as the rest of it, it doesn’t reflect what I recorded.”

https://longreads.com/2019/01/29/shelved-fiona-apples-extraordinary-machine/

It gets even weirder: Peter Kehew who also worked on the album says that it doesn't match the version Jon Brion recorded (which he has heard) and insinuated that a fan may have "modified" the tracks. 

\> However, what's interesting, and you may have heard the controversy about the leaked album, what leaked out to the public is definitely not the record that Jon Brion made with her. It's some versions of it, or maybe rough mixes, but I've heard the finished thing and that's not it. Some of those things that leaked out are actually modified, not even stuff Jon did. Somebody added parts to those things at home - a fan did it or something. So a lot of those things are not what the label heard and what Fiona and Jon had in it. So that's a very strange thing and we've never really talked about it. But I do know for a fact that what leaked out is not the record that Jon Brion was intending. I would love for his version to get heard someday, but it's not that different, nor is it the same. You know, people are judging on what it was supposed to be.

In other words the narrative surrounding this album is totally false. Nobody involved wanted it leaked, nobody knows who leaked it, we’re not sure who produced the tracks and it’s not even clear who recorded parts of them.

https://www.songfacts.com/blog/writing/the-untold-story-of-fiona-apples-extraordinary-machine

One of my favorite unsolved mysteries: what is the true nature of the “John Brion Version” of Extraordinary Machine, which supposedly wasn’t actually produced by John Brion?