I don't see them wanting to write code for 2 different OS's. I'd see it more likely the whole lineup jumps ship off Intel and go pure Arm, than they would run Arm and Intel. That's if they were to do something like that, which I can't see.
They already have 2 OS to support. The recent renaming seems to suggest they may be wanting to get that down to one.
Having said that... they have been filing patents the last year or so that seem to suggest a few things about what they have running in house to me.
They have been granted a handful of patents regarding SOC GPUs setup in such away as to take some specific load from the CPU with no software input. (the patents describe a system that detects specific type of math requests and starts shunting them for calculation on free GPU threads.) The patent in question claims its intended use is for debugging. It seems more likely to me it is describing a SOC with a built in GPU capable of doing some float point when needed. In another patent it describes almost the same thing in reverse... with a second GPU and or CPU taking work loads from an external GPU. Neither of these seem likely to have been cooked up for debugging of games as suggested by the patents. More likely they are being used for some in house special project... which may or may not be ARM based SOC running desktops. 9,390,461 B1 9,292,340 B2
This 9,280,471 B2 is about SOC cache systems... and may not be related to the others in anyway, however it seems to me it could possibly solve L2 cache issues involved with splitting instructions with a GPU out of order. In my mind this patent seems to add to the idea of them looking to use the SOC GPU cores as co processors.
I don't have the patent number for the one patent I was really looking for. It was granted early this year but I couldn't find it doing a quick look. If I find it later I'll edit. That patent describes a system that sounded very much like "code morphing" that was used by Transmeta to run x86 code on the crusoe chips. If apple does have a "hardware" code solution much like transmeta used... and a solution for CPU/GPU load sharing baked into their new SOC. I believe they could replace Intel in all there machines with out having to touch one line of code in the OS or third party software. The only question would be performance. I am not sure unloading work to a SOC GPU would allow them to equal the performance in the highest end Intel parts... I'm pretty sure however they could easily equal Intels mid range and down. We'll see what happens I would imagine pretty soon. Apple is long overdue in their refreshing of their line, if ARM does become the word for Apple.. it will make for a very interesting 2017-2018 for the industry if the performance is there. (and I couldn't imagine they would really go that way if it wasn't)