You have to keep paying the engineers even after you buy out the company, you know. Having to buy PA Semi just made it more expensive for Apple to develop the chip. This is definitely a long term payoff horizon.
I thought EVERYTHING was done by Jobs. Surely he's not paid that much! There are no RnD costs, Steve just dreams it all up.
Jobs' salary is $1 a year, and yet he is often cited as the most valuable CEO in the world. Though to be fair, every so often the board awards him with stock options, airplanes, and all kinds of other bonuses.
Generally for internal accounting you will mark it up to a fair value anyway as it makes it easier to see where costs are allocated and which divisions are profitable, but doesn't change the overall profitability of the company