Best Digital Interface

The answer is very simple.  You have to listen to your system, using various cable connections and decide what sounds best to you.   There is no correct answer for everyone.  

I decided on a music streamer with BOTH USB and AES/EBU digital outputs to my DAC.  I listened AND listened to both USB and AES/EBU connections for several weeks.

After weeks of switching back and forth, I prefer the AEB/EBU connection from my Aurender music server to my DAC.   To my ears, the music sounds slightly better using the AES/EBU Connection.   

Without USB isn't the clock in the Node 2 running the show?

Yes, but:

1 - You can't put USB in the middle and have it magically control the output of the coaxial cable.  The coaxial signal (or optical) is one way only. 

2 - The only reason this was ever needed in the first place was to improve upon mediocre clocks in the transports by replacing them with the superior clocks coming out in the DACs. So, if the transports had perfect clocks, asynchronous USB would never have been needed.  These clocks are now better than they used to be.

3 - There are clock regenerators, like Wyred4Sound's Remedy, and it does work and it is effective but only up to a point. It works a lot better with old DACs than new DACs which have better clock locking circuits.

If your transport is providing S/PDIF, it's never a good idea to convert this to USB.  The target DAC will have to re-convert back to S/PDIF and I2S anyways, but now you have timing problems since USB is really a data packet interface and not an audio/timing interface.

The RME --might-- be re-clocking the S/PDIF data, but the S/PDIF data from the Node 2 is already clocked using the sample rate of the original music data.

I'm not familiar with your RME, I never heard of a dac that didn't reclock S/PDIF. I'll take  look at the manual.

30.3 Digital
  Clocks: Internal, SPDIF In
  Jitter suppression of external clocks: > 50 dB (2.4 kHz)
  Effective clock jitter influence on DA conversion: near zero
 PLL ensures zero dropout, even at more than 100 ns jitter  Additional Digital Bitclock PLL for trouble-free varispeed ADAT operation
  Supported sample rates for external clocks: 44 kHz up to 200 kHz
 Internally supported sample rates: 44.1 kHz up to 768 kHz

Maybe I'm a bit dim, but this section of the manual states that this DAC controls jitter of all formats.