It's like he views playing guitar as another form of art.
Tool is a rhythm based band where the roles of the instruments are reversed and non-traditional. The drums are the lead, playing polyrhythms, odd time signatures, and odd meters. The bass also plays a bit of a lead role, while keeping that groove and the timing on point. The guitar is more of that sonic soundscape and atmosphere and has more of a Special Effects role. the vocals are more of a backbone, and help keep a melody that plays along with the drums.
The one song where this is heard is Intention. It's basically one giant drum solo, with nice atmosphere in the guitar, while the bass keeps that rhythmic harmony. I like how this song has this electronic vibe, and goes well with the lyrics, hinting at how we humans are like apes, almost like the ones in 2001: A Space Odyssey, with the discovery of Technology.
I don't mind that at all, because he has created some amazing soundscapes with the guitar. I hear it more in 10,000 days. And I quite enjoy what he has done and created in terms of sound and atmosphere.
At times, I think he does those 0-3-5 riffs, just to keep time for Danny and Justin to do some lead parts and jam away.