Actually apparently Magnus did know of the Webway project:

“Me? No, I never lost contact with my father. We spoke many times before he ever set foot on Prospero. That is a bond that none of my brothers can claim. As our Legion departed Ullanor, I communed with my father and told him what I found on Aghoru, a hidden labyrinth of tunnels that pierce the immaterium and link all places and all times.” Magnus returned his eye to the stars, and Ahriman kept silent, sensing that to intrude on Magnus’ introspection would be unwise, though the ramifications of his discoveries on Aghoru were staggering. “Do you know what he said, Ahzek? Do you know how he greeted this momentous discovery, this key to every corner of the galaxy?” “No, my lord.” “He knew,” said Magnus simply. “He already knew of it. I should not have been surprised, I suppose. If any being in the galaxy could know such a thing, it would be my father. Now that he knew I had also discovered this lattice, he told me he had discovered it decades ago and had resolved to become its master. This is why he returns to Terra.”

A thousand Sons, highly recommended for both insides in Magnus/TK and pure awesomeness