Dick didn’t intend for Transmigration to complete his VALIS trilogy. He originally thought it would be a counterpoint to any mystical ideas in VALIS, but he surprised himself when it followed through on the themes of that book.
At the end of Transmigration Bill thinks he is Christ, which Dick admits is crazy, except it also could indicate Christ’s return in the Parousia. He uses Angel (who he says is based on Ursula Le Guin) to illustrate that intellect can only take someone so far, as Angel rejects Christ at the end of the book. He calls the novel “a damning indictment of pure intelligence lacking faith.”
He tries to explain his “meta-abstraction.” What we perceive as reality is actually just a signifier pointing to Valis, which is the true reality. The only way actual reality makes itself known to us is by the perturbation in the reality field. He also says he can’t put any of this into words, which is probably why it doesn’t make too much sense.
I think he is saying it’s impossible to see true reality, and what he saw in 3-74 was the real world converted into the information that we think of as reality. It was a sign pointing to a pure abstraction. He’s been trying to understand reality based only on its signifier, which is impossible. The absolute or phenomenal world is unknowable, although he is able to point to it.