The settings in the guide include updating to the latest Apple firmware as soon as the device is bought (this is something I'm under the assumption that happens as soon as you connect the new phone to iTunes anyway). But it doesn't hurt to make certain that the most recent firmware is installed, currently 2.2.1.
Most of the advice I do agree with, and it will make your iPhone, or fleet of iPhones, a lot less fun to use. I mean, the benchmarks will make the iPhone more secure.
You can grab a copy of the benchmarks here.
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