Almost every battery in a phone is a 'non-standard' shape, even including when you could pull the back cover off and swap batteries. Companies have been making custom batteries since the dawn of the cell phone, pretty much.
>> If additionally the OEM sued anyone who made batteries in that shape it would get an even lower repairability score.
I'm not aware of this. Source? Making knockoff components using Apple's logo and such is not the same thing.
>> If on top of that the car was designed to turn on the check engine light if its battery was made by anyone other than the OEM then it would get an even lower score.
Where, exactly, is this message on an iPhone? You mean the single pop-up window, and the notice in the settings menu (that you can easily ignore)? Yeah, not the same thing. It's unobstrusive, yet visible enough so a person who buys one knows if they have 3rd party parts in their phone.