The assumption I'd made was that they'd left the actual core mostly alone. They've gone a lot further than everyone else in what they've put around it though, e.g. large caches and other accelerators.
I'd be interested in being pointed to any references as to what they've actually done, not that much information is likely to be public domain.
My source is "I know somebody who knows somebody who works in Apple's hardware design team" so take it with a grain of salt but it seems that their core is almost entirely custom, or at least customized to the point where it's effectively a different core.
And it makes sense for them to do it too, they clearly have the money and people to pull it off and it gives them a big competitive advantage. It's not for nothing that they push for ARM on the desktop as well, this way they'd have a tighter control on their ecosystem than they've had for decades (maybe ever), both soft- and hardware.
I'd be interested in being pointed to any references as to what they've actually done, not that much information is likely to be public domain.