Yes, expectations affect perception, but that's not news.
Different guitars offer a different platform sound to the player, who then uses his or her technique to get different sounds out of it. People have an equally hard time identifying which mic or electronics were used to capture a vocal on a recording, but the mics do sound different. Thing is, the voice sounds more unique than the electronics, and that's what the ear concentrates on.
The player is the X-factor in the sound of the guitar. The player makes different guitars sound more alike because the player is taking the information the guitar is giving with each note, and manipulating with his/her technique to achieve a certain sound.
The listener is processing pitch, dynamics, tone, the sound of the room, the sound of the mics and recording equipment, the sound of the amp, the inherent tone of the player, etc., all at the same time. No wonder it's difficult to tell guitars apart on recordings. But the listener isn't part of the player's feedback loop as he or she is manipulating the instrument and its components to achieve the player's sound.
Finally, our ability to retain very detailed information about tone differences to be able to identify which is which when switching between listening to two instruments is utterly lost after only a few moments. A/B tests have that built-in limitation. In addition, A/B testers suffer from ear/brain fatigue after only a few playbacks. Both of these limitations have been proven. Add in the vagaries of the recording process and you're really screwed as a listener being asked to identify certain tones.
There are lots of differences between the basic tone platforms of various guitars that a player uses (or must overcome) to enhance the playing experience that may or may not show up on a recording.
But all you have to do is look at a waveform analysis of a note plucked on two different electric guitars and you'll see differences that the ear can hear.
Yes, different neck woods will provide a different base tone. Yes, you can hear differences between bolt on and set necks as you play them. Yes, these differences affect what you might do with your technique, and even enhance different styles of music (for example, chick'n pickin' on a tele, with that compressed attack of a bolt on and fast transient of maple on maple).
Does your '61 SG sound different to you than, say, your PRS with RW neck? Of course it does, unless you're completely deaf. Certainly your expectations are different, but there's also a real difference in sound.
Can you identify it on a recording? That depends on the limitations of the recorded medium. And trust me, there are many, many limitations.
And among the limitations with electric guitar is the amplifier, that influences the sound to a huge degree.
Another limitation is that it's very difficult to pluck a string to the same amplitude and in the same spot on the string repeatedly. You'd need a machine to do it. And amplitude and where you pluck changes tone.
And the more distortion the amp adds, the less difference between the guitars you can perceive.
