Are the Master Program & Certificates I am about to embark on relevant to my career & academic plan?
Did the scientist know that you were thinking about doing a PhD or did he or she think you were staying in industry? 

The certificates may be good ways to see if you're interested in the field, but I think they'll be almost worthless in PhD admissions. The exception might be if the certificate is given by a well-known, reputable university and the program itself has an excellent reputation. In addition, it might need to be known by one or more faculty members at the universities that you're applying to. 

Do some searching here for related questions like this one: PhD in pure mathematics for a student in computer science

And a more general question: Undergraduate research field different from PhD field