It was such a big deal because Apple has a monopoly on „acceptable“ replacement batteries (the system shows a warning when you insert a 3rd party battery), and they charge 3x their actual worth.
I'm surprised to be defending Apple on this, normally most things they do seem pretty anti consumer and leave a bad taste in my mouth. But in this specific case I really don't think they deserve the scorn.
The warning is there for that reason. The phone still works with 3rd party batteries.