It's a choice. The layout isn't PCA, it's a force-directed embedding (ForceAtlas2). This acts directly on the directed graph of pages and their links, I think you would need some other representation to do PCA.
You could likely run ForceAtlas2 in 3D or higher and get better clustering fidelity, but that obviously makes visualization harder.
Did you actually read the article? Multiple times, they talk about how they're just trying to find a smooth, comfortable workflow and don't need every detail perfect (at least initially).