I'm going to clarify something on your last point. Both rebates that I'm talking about here are purely for the GST, or the federal component of the HST.
In the case you describe, the entity would not be allowed to claim the book rebate. Usually, when there's a supply of a course and a supply of a book, the books are supplied separately from the course. The intention from the policy side, since the inception of this rebate, was always that if the books are to be sold for consideration, the book rebate is basically not applicable.