Woa, that's unexpected.
Intel and Apple probably signed this contract quite a while ago, though, maybe at least 18 months ago. If Intel wouldn't have gotten this, it would've probably shut down the entire mobile operation, including the modem division (it would've probably sold it off).
In reality, Intel is killing Atom, because Skylake has more or less spec'd it out of existence. Atom was an attempt to do x86 with a low power, smartphone/tablet budget, and it sacrificed a lot of performance in order to fit into that budget. The result is a 2.5w Airmont chip.
Intel have also been focusing on low power with their Sandybridge/Haswell/Skylake Core line. And the result is a 3.5w Skylake chip, that has over twice the performance of the Airmont chip. 3.5w is still a little large for a phone but it's small enough for a tablet. In the next generation or two, intel will shrink the Core architecture down to something which fits in the 2.5w power budget for a smartphone.
Basically, Intel are killing Atom because it's no longer better than Core in any way. They will regroup and launch new SoCs in the future.