[sjdv1982]

I was dragging to rotate it before I realized that it was 2D...

Are there really two principal components or is that primarily your choice of visualization?

[tfpgh]

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.