Why wood matters... ?

A pickup is also a microphonic device. If I get close to the pickups of my 1965 SG Special and speak, my voice will come through the amp. The pickups will in most cases reproduce some of the acoustic sound of the guitar. The microphonic nature of pickups contributes to what we hear as feedback, and this is why hollow body guitars tend to feed back more than solid body guitars.
I catcall whistle into my Hollowbody’s pickups when my wife walks by 😂
 
My PRS Hollowbody with modern pickups (SDs) sounds different than my Majesty with Dimarzios - but I don’t think anyone would be able to say “that’s a Hollowbody” in an A/B recording of my metal riffing, they’d just go “A sounds different than B”

The key here is 'metal riffing'. You're mostly hearing amp distortion and harmonics, not guitar. Try playing the two clean and listen to the differences, I think you'll find they're even more substantial, but if we can say 'A sounds different from B' we are acknowledging audible differences, and it becomes a matter of degree.

And even the Strat vs McCarty thing, they’re different scale lengths on top of different body shapes and maybe different tone woods, so there’s a lot of variables there.

Yup, there are certainly variables. It can be a matter of degree.

A few years ago I had a maple neck 594 Wood Library and a mahogany neck 594 Wood Library model with the same pickups in my studio at the same time, and got a lot of play time with them.

The two guitars didn't sound the same. And the differences were as-expected, which is why I bought both.

I also had two CU22 Soapbars at the same time, one with a maple/maple neck, the other with a maple/rosewood neck. Again, the differences in the fretboards' tone alone were exactly as expected, and 100% predictable.

But since 1967, I've played an awful lot of guitars, and owned scads of them. I think the tone wood differences weren't subtle.

However, I'm not a metal player. I'm a 'clean to edge of breakup' player for the most part. So my perceptions post-amplifier are going to be different.
 
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