Basically, the procurement process for supercomputers is like this: the buyer (e.g. a DOE lab) will ready a portfolio of apps (mostly simulation codes) with a specified target performance. Vendors then bid for how "little" money they'll be able to meet that target performance. And of course the vendors will use the most (cost/power) efficient hardware they can get.
The reason why we're no longer seeing custom built CPUs in the supercomputing arena, but rather COTS chips or just slightly modified versions, is that chip design has become so exceedingly expensive and that the supercomputer market is marginalized by today's mainstream market.
Also, the simulation codes running on these machines generally far outlive most supercomputers. The stereotypical supercomputer simulation code is a Fortran program written 20 years ago, which received constant maintenance in the past years, but no serious rewrite is viable (costs exceed price of hardware). So vendors will look for low-effort ways of tuning these codes for their proposed designs. Sticking with general purpose CPUs is in most cases the most cost efficient way.