I saw a guy I know at a wedding a few weeks ago who works at Shaw Research, and I asked him about this. He didn't give explicit details on custom vs. commodity performance, but he did say they had machines up and running and giving novel results.

I doubt it is fair to say they are ignoring software improvements. I saw Shaw talk about the machine architecture and he had a lot to say about balancing programmability for later software improvements vs. specialized computational resources. Also, it was his algorithmic improvements, the "neutral territory" methods, that were inspiration for the machine. Are NT methods still state of the art for molecular simulation?