#1
My specific question is: how did he get the strings to sound somewhat palm-muted when he wasn't palm-muting?

Like, less sustain.

Don't how to explain it further.

Does it have something to do with the humbuckers?
#2
I'm not very clued up on Black Francis' style but I'd guess he muted the strings with his fretting hand.
Guitars:
EVH Wolfgang Special LH
Gibson Les Paul Studio 2013
Ibanez EW20LASE-NT LH

Effects:
BOSS GT-100

Amps:
Fender Hot Rod DeVille 410
Laney IRT Studio + 112 cab
#3
Hmm, I doubt that, to be honest

Because I think even the open notes sound muted

There's something special about his Telecasters
#4
What makes you think he wasn't palm muting? Also, what makes you think you can't mute open strings?

If you could post an example that'd help, since nothing you've said suggests that this is anything other than muting.
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#6
I can't really see much in those, personally. But as mentioned before, there IS such a thing as muting with your fretting hand.
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#7
He doesn't have a solid palm mute on there, but he could still be killing the sustain with his palm as he strums, or muting with his left hand. I think you're fixating on a relatively improbable answer rather than the more likely technique-based one.
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