Besides the long history between those companies, Apple also has an architectural license, so they just take the ARM instruction set and completely build their SoC including the different CPU Cores themselves.

Other ARM licensees often don’t design the entire chip themselves, but instead use the ARM-developed CPU cores of the different Cortex families and maybe also the Mali GPUs and other adjacent ARM chip designs for periphery, memory etc. so they not only buy the license rights to the ARM instruction set, but also readily designed SoC components as well.

Those licenses are usually more expensive, but lets you make you SoC much faster and you don’t have to design you CPU and maybe GPU and whatnot yourself. Apple goes through all that trouble to maintain full control over their SoC, so it makes sense that they pay less royalties to ARM because they don’t need to use any of the ARM Cortex design and such.

I think Apple had (or might still have) a similar deal for their GPUs, they licensed the PowerVR GPU architecture from Imagination Technologies but I believe they have been using custom GPUs for a while now