tfpgh

There's no reason to think the Millenium Problems aren't vastly different levels of difficulty to solve. Despite them all being hard, some may be much harder than others.

This isn't quite true, problems in NP can still require exponential time to solve.

Solving an arbitrary NP problem looks like first reducing that problem to SAT and then solving the equivalent SAT problem. We know (via the Cook–Levin theorem) that any NP problem can be reduced to SAT in polynomial time, and we now know that solving SAT is subexponential in terms of the size of the SAT problem, but it's possible for the conversion to SAT to grow the problem enough that it's exponential in terms of the original problem.

This is amazing!

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.

A few days of work doesn't matter over years.

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).