I understand your logic there; the only pitfall I can potentially see is that it kind of creates 2 manuals for the user to have to move back and forth between which is not necessarily a problem if:

* the person reading the user guide knows they need to go to the 2nd manual
* the 2nd manual is as clear & concise

Thinking about it from a new user perspective, there may be a consideration of the "one stop shop".  I go to the user guide, I get the answer, end of transaction.  I agree that it does make the user guide a higher maintenance proposition, but at the same time, it does accomplish 2 other things:

* It distills all relevant instruction and documentation into a single location
* The API docs are going to cover a lot of protected and private methods that may clutter the user's ability to quickly navigate to the specific information, particularly since the API methods & properties are not listed in logical order (e.g. alphabetical). 

Just a devil's advocate thought process to consider.  I can do it in any way that is acceptable.