These problems are endemic of the wider industry as a whole - music is having some major quality control issues and has been for many years. People are abandoning traditional recording methods, and adopting quick and cheap recording processes. Everything is recorded badly, and super compressed.
I dont know for sure as im not an expert but a lot of her vocals sound super compressed which means they werent recorded properly in the first place - OR - she purposefully allowed herself to be autotuned.
It breaks my heart to think what Rebel Heart could have been had she had time to produce it in the way she intended. Im not saying it would have been hugely different for sure, but at least she wouldn't have been rushed and had her decision making prejudiced.
The sessions probably had the best selection of songs she has recorded since Ray Of Light, but it was poor production that let it all down - something that ultimately she always got right - even if it was bringing someone in at the last minute to oversee quality control as an over arching thing - like Nellee Hooper did on Bedtime Stories. I think she may have intended Kanye to fulfil that role, and while i dont hate what he did with some songs, he ultimately wasn't invested in the project.
One thing we can say is that Mirwais is an audiophile so i do expect these problems to be eradicated somewhat with his re-introduction for the new record.