In Rage Against The Machine's first album (Rage Against The Machine) I frequently hear Tom Morello play with several "weird" scales. A few examples: Take The Power Back, Settle For Nothing, ... I wonder in what scale he plays over what key. It sounds kinda minor over a major key, but that is a guess.
Okay, I only got a chance to listen to the first of your suggestions so far, Take the Power Back. It's interesting what you say about the relationship between major and minor, with respect to this song; there are other semitonal/chromatic relationships too. I only listened through once, but here are a few thoughts about the pitch use and harmony of this song.
Before I say any more, the song seems to have a root somewhere between D and Eb; to keep things simple I'll refer to D as the root…
Most of the riff material seems simply to be based upon a D Minor Pentatonic. But already in the intro you have some interesting pitch relationships. The bass has D Minor Pentatonic notes, but the guitar has a descending chromatic line of chords (4ths, I think, which creates some interesting relationships):
(These notes show the pitch use, not necessarily the right octaves and definitely not the right rhythms!) So, already this is pretty weird. If we analyse the guitar chords in terms of the root note, D, we have a maj7 chord above a minor bass line, which drops by a semitone to a m7 (and then 6/9 to b6/b9, if you like…) Descending chromatic and major/minor relationship - more of these later…
Okay, for much of the next minute and a half we are basically in D Minor Pentatonic territory.
Then at the Chorus, at about 1m30s, we get D7#9 chords in the guitar part. And, of course, these are effectively seventh chords with major/minor thirds:
(Yes, I know a #9 would theoretically be an E# here, but we "hear" a minor third…!)
When we get to the guitar solo, the riff parts stay on D Minor Pentatonic. Here the solo guitar starts by using predominately D Aeolian and then moves very clearly to D Dorian. (There my be a few notes outside these, but I couldn't hear any or many…) Right, so both of these are minor modes, over a minor bassline - so no big deal huh? Well, you clearly hear the upward chromatic movement from the use of the minor 6th in the Aeolian to the major 6th in the Dorian. And, of course, they both fit with the supporting D Minor Pentatonic, as this has no 6th degree.
After the solo we get a new riff, and this one has a very clear descending chromatic motif:
But my favourite moment, in terms of its audacity, is the whole section based on a C pedal note (after the second Chorus). Although only four pitches are used here (C, E, F, G - loosely outlining C to F/C chords), we feel fairly strongly that the music has moved to C Major, certainly not in D minor, anyway. But in terms of the overall pitch usage, these four pitches are also found in D Aeolian, D Dorian and D Minor Pentatonic - we haven't actually gone anywhere, pitch-wise…
Obviously, this isn't a definitive answer for you, as I only listened to the one track, but hopefully it starts the ball rolling...
The Guitar World Lesson with Tom Morello doesn’t directly answer this question, but it offers insight into why Morello makes the composition choices that he does. Specifically, he describes how his composition style is rooted deeply in experimentation, with several concrete examples. Essentially, Morello spends a lot of time simply playing around with guitars, filters, amps, and other equipment, and whenever he discovers an interesting sound, he makes a point of making it reproducible so that he can use it in performance. The Guitar World lesson focuses more on weird effects like “helicopter noises” than on his key and chord choices, but it’s clear how the same process of experimentation would lead to both.