So its been a handful of days, more "break in" happening, and a couple emails with Alvin @ Vinshine. He was kind enough to answer my questions rather quickly, I can only imagine how many emails this man has to answer from noobs like myself, god bless him.
So here's my understanding:
The Bluesound Node ( I have the latest version with USB connection) might have something funky going on with the coax and Toslink outs that just doesn't jive with the Pontus Dac (maybe other denefrips dacs, too) The Pontus just cant make the info it is receiving from coax and Toslink outs on the Node sound as good compared to when it is receiving from the USB out, like it can't correct the information properly. "If the signal that's feeding into the DAC is of poor quality, the DENAFRIPS DAC can't correct the information". I went back and forth and the difference is NOT subtle. Since "the USB, on the other hand, is asynchronous, the data retrieval is based on the clock of the DAC" , the Pontus now takes full control of re-clocking and correcting the info on its own, producing a superior sound quality. That is the answer.
So in my estimation, if you are using a bluesound Node to feed a denfrips dac, unless you are using the USB OUT on the newer version, you are NOT getting the full potential out of this pairing. Obviously, there are better streamers that will produce better results, but if you are using a node, make sure its the new one with the USB, or strongly consider upgrading. That's just my $.02.
Since making the change to USB, I am now very happy with the improved sound as compared to my other Dacs.
Hope this helps. Thank everyone for your advice!