Its not that simple. The A9X is a relatively big chip with lots of space dedicated to the GPU. Its 150 mm2 compared to something like the smallest intel skylake chip which is 100 mm2. This is to say that its likely more expensive to manufacture the A9X. The graphics score of the A9X is certainly impressive, but we don't have a wide range of benchmarks that compare the performance of the two. We also don't know what the performance per watt of the A9X is.
In things like browser benchmarks, a core i5 is still much faster than the A9X.
Your configurations don't make a lot of sense. Apple A9 + Polaris 11 would be putting a ~ 5 W CPU with a ~45 W GPU. Probably much too GPU heavy compared to a 25 W Intel Iris chip.
If Apple did leverage their own processors in the mac it would likely try and decrease the size and increase the battery life. You can already see them doing that with the A9. The A9X goes in the big iPads with extra graphics performance and the smaller and slightly more efficient with less graphics power goes in the iPhone. It would be fun to see this in the mac but I its still a side-grade and we its still unlikely Apple can scale this up to desktop class speeds. Could Apple make a chip that supports PCIe graphics? What about 64+ GB of memory? Thunderbolt? Its not that easy to create a platform like intel has.
AMD is going for a strategy like this where they can put a Zen CPU and a Polaris (or other future) GPU on the same package. If their CPUs can become competitive on the efficiency front than it should be a great way to tailer the CPU + GPU thermals and performance for exactly the product you want. This way you don't have to spin a different chip for each CPU+GPU combination. Imagine a Mac Pro the size of the mac mini (although cooling that would be a nightmare with all that thermal density concentrated in the tiny CPU/GPU package).
Apple is limited to the same manufacturing process as everyone else (except Intel). If Apple is stuck on 16 nm again this year the A10 will probably only be slightly faster.