The 30% "apple tax" on their App Store is not a major way that Apple makes money (more on this in paragraph 2). This leads to the conclusion that Apple is not attempting to hobble stores that undercut them: they simply like using their control of the store ecosystem to maintain the quality, simplicity, and consistency of the experience that allows them to provide to their customers, with the nice side effect of giving them massive leverage over their largest competitors and power over many external markets. I'd thereby reverse the order you have.

Checking the numbers, the profit margin on an iPhone is a little over $170, while the profit margin on an app is <<$1; most of the people I know who own an iPhone have purchased at least two of them (an upgrade a couple years later) and have purchased maybe, at most, 10 apps. If you check the Apple quarterly earnings reports Apple doesn't even bother separating App Store sales from iPod accessories: both are a tiny line item in comparison to the profit they make on their actual profit center (core hardware).

However, for content resources, such as books or music, the story is much different: I know people who have purchased many thousands of dollars of music, movies, and television shows from iTunes over the years. This is enough that the iPod and AppleTV can be effectively subsidized by iTunes (something you don't see Apple doing with the iPhone: they make certain to get their profit on that at the point of sale, possibly plus a carrier subsidy).

This is why this issue starts coming to the forefront for services like Rdio and Kindle: those actually hit Apple where it hurts, so Apple would prefer to use their control to hobble their opponents. But, Apple doesn't really want 30% of the revenue from these sales... it would be much better for Apple if they just went away, and people used iTunes instead. (I make this clear, as that is why I then don't feel it accurate to use this as an argument for the 30% being a primary concern.)