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There is no definitive list of differences between the 1st and 3rd editions. The 1st edition was written for WordPress 2.9 and the 3rd edition was written for WordPress 4.2, so as you can imagine a lot has changed between versions.
A few notable differences are the latest edition includes Custom Post Types and Taxonomies, which were not in WordPress when the 1st edition was released. The latest edition also has an entire chapter dedicated to WordPress Multisite, which also wasn't included in the 1st edition. We even dedicated a chapter to Using WordPress as an Application Framework.