This is not really about VLSI style hardware knowledge. The 'processor affinity and NUMA' config is all about minimising the cost of memory access, and maintain

This is not really about VLSI style hardware knowledge. The 'processor affinity and NUMA' config is all about minimising the cost of memory access, and maintaining cache consistency. They want to make sure that processes aren't continually being moved to different cores or accessing memory that is further (slower) away, to minimise latency. The 'clock synchronisation' talked about is probably not at the CPU clock level, but rather the wall-clock time, using GPS receivers or atomic clocks and NTP servers to ensure all involved servers are synchronised.