There is such an overhead when dealing with an external company. Integration projects are rarely fun. I postulate that having your hardware designer report to the same guy as the chip designer makes the process much more streamlined. No waiting for contracts / bizdev, being scheduled with competing projects, et cetera. The powervr chip in A9 could be configured to support OpenGL (non-es), but the TI Omap series has it set up for OpenGL ES instead. Now, if you are apple, you could probably get TI to change that for you... but then you're talking about contracts & process management and integration once again. Wouldn't it be nice to just set directions and have it done?
And the arm platform is quite an open platform. I bet any successful company can work with big semi companies to tweak chips.
The biggest advantage is secrecy.If apple has some unique feature - it gives them the time to secretly do research on processor architectures for it.
But not a lot of value for features everybody are looking for. in this case open r&d is better.