In the sense that they cover the same functions and controls as do the Nikon manuals, there obviously are some similarities. In the sense that the byThom books actually explain not only what a function or control is used for, why you might want to use it, and what things you need to know in order to get the most from it, no, byThom books go far beyond what Nikon supplies in their user manuals. This is most obvious in areas such as focus or exposure and setup, where the Nikon-supplied manuals don't tell you much at all about how the system is making its decisions and why that might be important to you.
Thom Hogan has been writing better instructional manuals, articles, and books for high-tech products for over 40 years, and his work has been acclaimed by many throughout that time. So much so that manufacturers have sought out his works and included them with their products (Microsoft and Fujifilm, for example).