Well if you’re asking me specifically, my short answer is…..beats the hell out of me. I’m still learning this hobby as I stumble along. I have some experience with instrumentation and electronics from the technical trade, but that’s not saying much.
That being said, an amplifier does absolutely nothing to the signal but "amplify" it. It does not manipulate it in any way shape or form. However, I suspect that the basic physical size and real estate that the separates have over a receiver will dictate the time and quality of gizmos the manufactures can design and install. I’m just guessing, but I strongly suspect that this alone will enable the sound to be “cleaner”. And this would be due to a higher level of isolation between electronic components. But sound different??? Warm or Bright??? No friggin way do I by that. It’s impossibility from a theoretical perspective.
Now pre / pros, and receivers? Absolutely. Just think about how the signal is passed from the source to the amp. It goes through the processor. This is where all the magic happens. Including tone controls. Just the different sound options that a person can make on an AVR (dolby, pro logic, etc…) is a pretty good indicator that the signal isn’t simply passed through, but manipulated.
