Even if the patent on the instruction set expired, that's only half the battle (if that). When you licence ARM you're getting both the instruction set design AND the implementation.
AFAIK Apple mostly only licenses the ISA and then runs a completely custom implementation, so in this case that's not relevant.
I think the sibling comment is more accurate: while the core of the ISA might effectively be public domain soon, there are plenty of extensions in common use that aren't. If you implement a custom x86 design without those a lot of software won't be able to run or it will run with significantly worse performance.
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.
