Looks like it’s not only pedals but also production techniques. About his solo album he said:
Every part that sounds like a synth is multi-tracked sustainer guitars, like the string-section of an orchestra. Even the deeper bass notes, is a Spanish guitar played in a way that sounds more like a sequencer.
That means part of the sound quality he gets comes from recording layers of single note parts that each sounds a bit like a mono synth and having them stack up to an “orchestra” type of sound.
There are two main components at work for his raw guitar tone: the sustainer system and the pedals. Using an ebow or sustainer does a lot to change the timbre of the guitar because it allows the guitarist to change the transients and envelope of the sound. It can be very hard to recognize a sound as a guitar when the initial picking noise transients and the normal attack/decay of the sound is removed. On top of that, a whammy pedal messes with the raw tone a bit, especially when the pitches are shifted by larger intervals. At in the memory man that he says he has on almost all the time, and the chorus and delay effects complete the change from clearly a guitar sound to what seems like a synth.
If you just have distortion, delay, and reverb on a guitar and simply roll off the volume, pluck a note, and roll the volume back up, you get a sound that might still be clearly a guitar but also could be something else. The sustainer and effects just enhance that to a great degree.