What kind of R&D is happening at Apple? I did a search with the keyword "research" on their job board and not much interesting turned up except for a few "Data scientist" positions.
In any case, this isn't really news, or even good reporting. Look at the rest of the financial statements: SG&A and R&D expenses have actually decreased as a percentage of net sales over the last two years. Apple is big, so the absolute numbers are impressive: but percentage-wise, this isn't even a blip. TFA is cherry-picking numbers and sensationalizing for page views.
See: http://files.shareholder.com/downloads/AAPL/2149923444x0x444...
In terms of units shipped, the iPhone and iPad vastly outstrip the Mac. And those devices repay investment in chip technology by establishing a marketing point of differentiation.
So actually, given the amount of free cashflow Apple has, it makes sense to spend up to a billion on embedded chips but not on desktops, where Intel has a far bigger lead on design and process.
There wasn't an issue at all with keeping up with performance. The problem was that IBM was pushing PowerPC more and more into the server space and Apple needed a roadmap that factored in laptops.
That being said, I would say they've built both their CS and EE capabilities to the equal of any other company in the world. Custom silicon, compiler tech in llvm/clang/nitro, the whole OS related stuff, etc.
They developed a new SoC in the A6, made the screen thinner incorporating the touch sensor which was novel and created new manufacturing processes for building the case.
All of these obviously flow to the other products e.g. iMac, iPad Mini.