Going by my past experience in participating in such threads, I desisted but Thirthankar's post about the third group stirred me up.
I'm not sure if you have come across a well calibrated set up of a SET amp + high efficiency speakers. I'm sure it will give you a different perspective of sound. My apologies if you already have, no offenses meant.
Well to answer your question, I have listened to some of the nicest stereo setups, including at Ascend Acoustics own studio. No doubt these were almost reference quality setup, especially the Ascend Acoustic setup. I have listened to some other AVR based setups, some were dedicated Pre-Pro/Amp setups and those were nice too. But I never got to do A/B comparison plus most of the comparison was based on memory. Which we all agree is not a valid way to do.
So my best comparison was at my home. My equipment is
AVR - Sherwood R-972
Amp - Adcom GFA 7500, 5 channel amp
Source - Marantz DV8400
Speakers - JBL 4410
Cables - Monoprice.
The JBL's are very high efficient speakers. My earlier receiver Onkyo 605 was able to drive the front 3 JBL 4410a and 4 JBL 8330 speakers without problem.
Now, Both sherwood and Marantz can turn off all the processing in Pure Audio. There is no display, no video processing, everything is shut off. I compared the listening following way.
1 - Marantz analog out to Adcom. No volume control in between. To get the level right, played a 60Hz sine tone, measure the db level using spl meter (It was quite loud)
2 - Marantz Analog output to sherwood. Its on Pure direct. Sherwood driving the speakers. To level match with 1 - played the same 60Hz tone, adjusted volume till got the same spl rating as 1.
3 - Marantz Analog out to sherwood. Pure direct. Adcom used as amp driving the speakers.
4 - Marantz digital out to sherwood. adcom used for driving speakers.
Now during these listening tests, there was some delay as well, in switching the cables etc. so its not lab grade A/B.
All these listening, I could not hear a huge difference. There were very subtle differences. Not a whole to jump at you or make you want to have it differently. But when I changed to test 4 and refined it bit more with Room Correction and different modes, I could hear lot of differences. Mainly could be because I was able to change it on the fly with a remote button press.
I called my few friends to test it out and not a whole difference to point out. On the other hand when we did A/B comparison between my earlier speakers and JBL's, same friends could point out the differences without problem. That told me there was not a whole difference as made out between the AVR and a dedicated amp. vs directly from the cd player.
I still have the adcom in the chain. Main reason for that is because the sherwood AVR has a current limiting switch in it, making it clip when all 7 speakers are driving. I haven't heard the clipping so much, but want to protect my speakers. That's why left the Adcom in the chain to drive the front 3 speakers. 4 surround speakers are still driven by Sherwood.
I know its my own test, but it did the work for me. Everyone has their own tests. But our experience need not have to be projected as reference to others.