Regarding PhoneGap specifically, which the book seems geared toward, for a short period of time Apple believed, erroneously, that the iPhone PhoneGap code was exposing unapproved APIs to developers, and were rejecting apps that used the platform. At that time, I think some devs were obfuscating PhoneGap and submitting the same apps, which were approved, so even then Apple were not objecting to anything actually in the iPhone PhoneGap code.

Apple have been in touch with PhoneGap devs since and clarified the matter; there's a good blog post here regarding that: http://nachbaur.com/blog/updates-on-apple-phonegap

Since then Apple have had a much more informed stance towards PhoneGap and have approved lots of apps using the framework (there's a list on the PhoneGap site).

*full disclosure - I work for Nitobi, who sponsor PhoneGap's development. Though the original link suggests using PhoneGap in its preface, there are competing platforms, such as Rhodes and Appcelerator, that also get through to the App Store.