I’m trying to evaluate the pros and cons of the various digital protocols available for mass flow controllers. Do you have a reference you would recommend?

I would strongly recommend you take a look at the “Digital Instruments & Protocols” document that Brooks Instrument published earlier this year. It addresses the advantages to be realized from a digital solution as well as a number of the considerations for each of the most widely utilized protocols. Here is a link to more information;

Digital Instruments & Protocols