Even the icons and color themes are the same on many screens. That by itself shows that Samsung copied Apple in prior product reviews as well. Kinda funny that they still had so many design discrepancies...
Sometimes the competition does it better but not necessarily the only right way, for example the email indicator on slide 20. In that case the directive suggests another way of improving the interface.
Whoever wrote this document did not want the devices to be too similar:
Strong impression that iPhone's icon concept was copied. Directions for improvement: Remove a feeling that iPhone's menu icons are copied by differentiating design. (last slide)
Wish they did that before putting the phone on the market...
I've not read the whole thing, but I've not seen any clear examples where they've had lots of choice in how to make things better without making things more similar to the iPhone. Now that's an impressive testament to the quality of Apple's UI design, but most of it is "obvious" - the problem isn't that it's hard to figure out that you'd like a "previous" button to go with a "next" button, but that it takes a lot of attention to detail to get this level of consistent quality throughout the product.
And Apple does that well, and Samsung at that stage clearly had not done all that great.
If Samsung had put in that attention to detail, the devices would likely have been a lot more similar from the outset.
But the bottom directives turn it into a PRD (requirements doc), and the directives themselves call for steps that make the devices much more similar.