@smilen - I use the DAC-V1 USB input. It has been such a long time since I tried the SPDIF. It would be hard in any case to compare the two as the signal path chain in my setup would be different. The DAC is in fixed output mode.
What I found earlier on was that even with the galvanic isolation, it was sensitive to the USB signal (e.g. changing USB cables, PCs, laptops etc altered the SQ] likely due to some noise infiltration. The DAC-V1 output was like a clear lens looking at a ‘dirty’ upstream!
This of course gave the opportunity to research how the fed signal could be ‘cleaned up’. The audiophilestyle website was very helpful in this regard even though there are a few rabbit holes there. In case you have not done so - if you do a search there you will find threads on the Raspberry Pi.
In summary every thing upstream that I have done now improves the perceived ‘background silence, sound stage focus, low level sounds and trailing decays’ i.e. enhanced the music soundscape perception. Keep in mind though that each change also can have its own sound signature (e.g. what power supply you use) so it is all personal preferance and there are some trade-offs.
Below is a newer picture similar to what I posted there some time back, some of the annotation would be for that site. Basically this is a control/endpoint 2-PC setup running JRiver on the two machines. The endpoint is an Intel NUC with the Audiolinux (proprietary) OS loaded/run from RAM. The control PC is an older one with Win 7, soon to be upgraded.
There are some brief subjective notes in the picture that I made to myself. I hope all this is of some help! The idea is to reduce the CPU load and isolate from the LAN using a bridge between the control and renderer, server.
I did ask J River at their forum for an expert view of why the SQ is better with this setup than that of either PC as a single- I only got a ‘frown and headshake’ -and the exclamation- audiophiles!
PS - I did try ROON a few years back, loved the UI but found the SQ to be a tad less than J River’s- hope that one day they can rectify that (from what I read, they haven’t)!