You know, I always assumed that using the two step process of printing to file then using distiller (rather than using the direct 'export to PDF' function) was to ensure that the distiller job settings were correct for the project. If I am reading your response correctly, particularly Good workflow through the entire process ..., you mean that once distiller has its options set (e.g. to the default 'Print' setting), then this is retained until you go in and deliberately change the settings again. So if you know that you will be creating a whole set of PDFs all with the same settings, it's OK to use the Export function?
I have used that watched folders option once when I was making a lot of PDFs (for a folio display) so I know it's a pretty nifty timesaver. But back then (well over 12 months ago), I had no idea about the preferred sequence for making PDFs by the 2 step method. Since I so rarely make a lot of PDFDs in one batch, I tend to use the 2 step method so that I know exactly what the distiller options are set to.