I can't speak for every DTRPG PDF, but the one PDF I got from DTRPG (TNE FF&S) was identical in quality to the PDF on the FFE TNE CD (note that DTRPG PDFs come with a watermark, the FFE CD does not).
With respect to the many other FFE CDs that I have gotten, some of the early CT CD scans had resolution issues which were fixed on the updated CT CD that FFE sent as a replacement ($7 for a replacement CD, but free when ordered with another product) and is now the standard FFE CT CD.
I can unhesitatingly recommend the FFE CDs as a great deal and a useful product. Even if some DTRPG PDFs turn out to be of better quality than the FFE CDs (which is very unlikely) any difference in quality will be minimal and not be worth the difference in price.
This is like deciding to buy a car one piece at a time and assemble it yourself vs buying a car pre-assembled. If you only need a small block chevy motor, then go to DTRPG, but if you plan on getting a whole car, then go to the FFE CD.