That statement appears to rule out an OS merger, which would be the easiest path to unification. Essentially, Apple created iOS by forking OS X, so the two operating systems already have much in common. Microsoft is moving in the opposite direction, converging Windows with the Windows Phone OS -- as people confounded by the new Windows 8 user interface will attest.
If Cook's word is good, OS X and iOS will continue to exist as parallel universes. Unification, if it happens, will harmonize the low-level hardware, not the operating system: Either Macs will get ARM processors or iOS devices will get x86 processors. Good arguments abound for both scenarios.
Why Apple is unlikely to switch the Mac to ARM processors For about two years now, the tech industry has thrilled to a rematch of the RISC-versus-CISC wars of the 1990s (embodied by RISC processors like the PowerPC and CISC processors like Intel's Pentium). The war fizzled on the desktop, and by the mid-2000s, ARM's RISC architecture dominated 32-bit embedded processing (especially in mobile devices) and Intel's x86 architecture dominated PCs and servers. Frankly, much of the current buzz is fueled by the industry's hope that someone, anyone, will mount a serious challenge to Intel, especially now that AMD is suffering another funk.
Compared with Intel, ARM is a puny company, but its licensing model is a force multiplier that allows ARM-based processors to outsell x86 processors by about 20 to 1. Anybody with money can license off-the-shelf CPU cores from ARM to design a chip or license the architecture to design an ARM-compatible CPU core. Several companies will manufacture those designs for you.
One of those architecture licensees is Apple, which is now designing its own A series of CPUs for iOS devices instead of buying chips designed by outside suppliers like Nvidia, Qualcomm, or Samsung. Intel will not license the x86 architecture, so if Apple wants to design its own Mac processors, ARM is the logical alternative.
One obstacle, however, is that no one has ever created an ARM processor as powerful as Intel's best PC processors. ARM fanboys tend to overlook this inconvenient fact. In theory, it's possible, of course. Mainly, no one has tried.
In the past, ARM and its licensees focused on minimizing power consumption, not maximizing performance. Low power usage is much more important for mobile devices than it is for desktop PCs, which draw their power from AC sockets and dissipate the heat using multiple fans or, in Apple's case, aluminum shells. Even lightweight notebook PCs can tolerate hotter chips than smartphones and tablets.