Oh, I believe that he's genuinely baffled as to why they didn't call him. He really is that clueless.
He wanted a break after Magnification, so they took a break. They called him in 2004, he agreed to meet with them, then blew them off. They called him again a few years later, but he said he was too sick to work on a new album (though not too sick to go out and tour with one of his side projects). Then he really did get sick, but said he still wanted to work on a new Yes album. When they called him for the sessions which ultimately led to this new album and tour, he wasn't interested. He was working on the Anderson/Wakeman album, but once that was done, and the tour, he was going to call them. They'd heard that before. He sold his share of the rights to the name Yes somewhere in there, declaring that Yes was done, finished, even though it wasn't his decision to make.
So after nearly 10 years of getting jerked around, Howe, Squire, and White (who own the name) got someone else to sing. And Anderson is baffled as to why they would do this.