That is one theory. ARM licenses both soft cores and hard cores. One theory is that Apple has a soft core license and is doing their own physical design. Physical design has a huge effect on power and clock speed (but not on the number of instructions per cycle).
Another theory is that Apple has an architectural license - if so they could conceivable design whatever they want that runs ARM opcodes, with as many cores as they want, and whatever architectural features they want. If that's the case, they conceivably would have a huge advantage over everyone else if you believe PA Semi guys are that great.
I know many of the PA Semi guys (and many of the non PA Semi guys who are now on that team). Some of them are very good. Some of them are highly overrated. Some of them worked on the original StrongARM chip for DEC (most of them, in fact). That's why I don't believe they are working on a PPC - their heritage is actually ARM. They were working on PPC only for a comparatively brief period.