They don't use exactly the same hardware since the XL/XL+ have a newer "secret sauce" version, that means the input stage design has changed and that, for how well and precisely it can be designed, can definitely lead to substantial differences in the audio spectrum, especially when it is interfaced with a high output impedance device like a passive pick-up.
I think who marks this as a placebo effect has no idea of how an analog electronic circuit works and how even a different resistor value can affect the impedances and the gain of that circuit.
Furthermore components' construction tolerances can come into play and I'm sure that we'd find slight (but probably non-audible) differences even if we analized two identical units with an oscilloscope and a rta.
And then I found this from Cliff himself that makes me believe the difference is expected:
https://forum.fractalaudio.com/thre...etween-axe-ii-mk1-and-mk2.97766/#post-1178592