I've come across some AVRs and preamps in the past with a tone defeat switch that when activated didn't sound any different than when the tone controls were in the flat posiition. One even has a mid-range control and another had two bass and treble controls with different turnover freqs. A well designed preamp section I think should have the tone control flat positions identical in freq response to that in a tone defeat or bypass condition. Those were "manual" tone controls in stereo preamp sections that didn't have digital processing electronics. These days, most, if not all AVRs use tone shaping and volume controls in the digital domain. From what I've heard, they convert all analog input signals to digital prior to the volume and tone controls and DSP manipulation. So maybe the behaviour of tone defeats and bypass versus flat tone positions are not the same these days.
If I recall right, some of the more expensive preamps I've seen today have "Stereo Direct" and "Digital Bypass" switches. Presumably these switches are activated for serious stereo listening; they bypass not only the tone controls but the rest of the digital processing circuits including bass management, digital channel delay and equalization settings for straight analog audio path.
And if you really want to achieve pure sound, some of the more expensive AVRs also have the video switching bypass and LCD display out switches. Otherwise these circuits are said to introduce noise into the audio path unnecessarily. Just a thought.