How does one distinguish between FAR/DFARS clauses to be flowed down by reference vs. in full text?

Not sure what you mean. Reading the clause should tell you, if there is such a requirement. Is there some general requirement about flowing by reference and flowing by full text that you are looking at?

Still not sure what the basis is for your question. But, does the following language to be included in the subcontract, help you?

The FAR and DFARS clauses cited below, where applicable by their terms, are incorporated herein by reference as if set forth in full text. The full text of all clauses incorporated by reference is available at http://www.acquisition.gov/