Where I think you might be missing in understanding is that the sound that you get out of your speakers has gone through a whole bunch of other electronics to get to that point.
I don't know your source material, so I can only guess. But lets for the sake of simplicity say you are listening to a CD. The CD player gets the digital signal and runs it through the DAC inside with whatever filters it wants/has and outputs that signal through your RCA cable. The back of your Pioneer has a some analog inputs but the internals of the Pioneer is all digital, so you are then running your analog back through a ADC to put it back into the digial domain, then the internal signal processing happens, it goes through any required pre-ampfication in a digital form and then back out through another DAC to the pre-out's on the back of the Pioneer. That then hits your amp and eventually the speakers.
There is a whole load of CRAP that the sound goes through inside the Pioneer before your amp sees anything. it is converted from analog to digital and then back to analog with who knows what filtering in the process. You can have a fantastic amp but if the signal you are getting out the back of your (effectively) pre-amp is corrupted from what was originally recorded, I don't care how good your amp is, you are not getting the original sound. Some pre-amps do a great job and sound fantastic. I personally found every one of my Pioneers to corrupt the sound and make it worse than what I experienced with my older Nak or my newer Anthem. Again, that just might be my experience and mine alone
Axiom: ADA1000, LFR1100, VP180, QS8, EP500, M3, M3comp
AudioSource: Amp One/A