Correction: I don't think it is necessary to warn the reader about non-standard RDF *every* time "generalized RDF" is mentioned.  But I do think it is important to prominently warn the reader once in each document, where the "produce generalized RDF" option is discussed.  

In the API document the most logical place for such a warning would be in the first paragraph of section 10.1: http://json-ld.org/spec/latest/json-ld-api/index.html#convert-to-rdf-algorithm .   In the Syntax spec, if the three suggested work-arounds for blank node properties are discussed (where it says: "For authors and developers working with blank nodes as properties when deserializing to RDF . . . "), then I think that would be the most logical and important place for such a warning, since that is where the use of the "produce generalized RDF" option is suggested.  (That is the location that this thread is currently discussing.)  I think those two warnings would be enough -- once per document.

The point of such a warning is to alert readers who may not otherwise realize that they would be generating non-standard RDF, because it is not at all obvious from the term itself that "generalized RDF" means non-standard RDF.  (If the RDF WG had called it "extended RDF" then it would have been more evident.)  Such a warning will help to ensure that users who make the choice to use non-standard RDF are doing so knowingly.  In fact, it would probably be helpful to include a highlighted warning box, explaining that "generalized RDF" is not standards compliant.