As a general rule, I'd recommend that you create your PDF files using Adobe's Save As PDF feature because they did create the original PDF specification and chances are the PDFs that they create are more optimized and better produced than the PDF files created by Microsoft.

But I'd only recommend that if you had a choice between the two. If all you have is Microsoft's Save As PDF feature, then just use that, it will create perfectly good PDFs.

At the end of the day, the differences between the two options will be minimal.