For the most part, I don't think it matters very much how you get the TrueHD/DTS-MA - bitstream (HDMI) or Analog output.
However, the sound level output (dB) may not be equal. In some cases, the bitstream may sound louder than the analog output.
I think as long as the sound levels are matched, you won't hear any difference between bitstream (HDMI) vs Analog.