I think in these cases, it's not the instrument that is sounding different, it's a person's variability. Your mood, how much noise you've been exposed to that day, your blood pressure, all these things can affect your system, including your hearing. So if you've lost some "highs" tonight, your Tele sounds good. In the morning, that humbucker sounds nice but the Tele sounds like an ice pick.
People can be very good at hearing slight differences, but when it comes to better or worse, we are affected by our biases. Since in audio there is no absolute "target" it's purely a judgement call.
I've seen cases where a race driver will comment about how a change has really improved the car, but then the stopwatch numbers say he's 5 tenths slower. Is that an improvement? Maybe, if it means you don't crash, maybe not if that 5 tenths puts you in row 11 instead of row 1. At least you have a real measurable target.