The headphone amplifier will not be "in the chain." The Lyr has a pre-amp and a headphone amp, much like a speaker integrated amp is a pre-amp and a speaker amp. When the line outs are used on the Lyr, the audio signal is being passed through the pre-amp much the same as when using the record out or pre-out on a integrated amp bypasses the speaker amp.
I would think the Lyr and speaker power amp setup would be more convenient because either headphones or speakers can be controlled via the Lyr's volume knob instead of having to deal with two different units for controlling the volume. I actually bypass the pre-amp in my HK 3390 that I use with my setup and use the main in input because it doesn't make sense for my setup to route the audio signal through 2 different pre-amps. Unless mrksgrn needs the extra features of the pre-amp in a speaker integrated amp, a power amp for the speakers like the XDA-2 would seem the better choice to me.
Primary benefit of preamping: controlling the volume. If it's built into the headphone amp and is feeding a power amp (or studio monitors that need a master volume control instead of fidgeting with each knob on each speaker) then it's not adding a headphone amp into the chain. If it was, that would be like saying an integrated amp is adding an amp in the chain and one should just hook up a CDP with no variable lineout directly into a power amp.
Unsure about the Lyr as I do not own any Schiit
. In the past, we would have used a common configuration being:
Source > preamp > power amp > speakers
The main purpose to reduce the noise floor inherent in the old tech power amp. However, technology has advanced since then, and a decent modern integrated amplifier should have no problems with noise or power output and filtering. Thus the actual benefit that I have concluded is that if you wanted some colouration in the sound (e.g. tube pre-amp with SS power amp) you could achieve that.
Of course, if the OP were to use the Emotiva power amp as he was considering, then yes he would need either an active or passive pre-amp to control the volume, this is not a benefit but a requirement
. Selection of the preamp is not a simple task, and you need to check the technical specifications of both the pre-amp and the power amp to ensure compatibility. If he did not like the synergy between this setup, he would have one more element in the chain to consider (i.e. the pre-amp).
However, since he stated that he was a novice, I recommended purchasing a integrated stereo amplifier as they have a clean signal, usually enough grunt to power 4 ohm speakers, and easy to setup. (plus it comes with a volume knob).