It looks like these extra metrics are dynamically created and added to the registry via the HBaseRPCMetrics.inc() and subsequently create() and get() methods. The org.apache.hadoop.metrics.util.MetricsDynamicMBeanBase class will update the MBean info if the underlying registry changes (see updateMbeanInfoIfMetricsListChanged()), but maybe this isn't being invoked everywhere it's needed?
The .inc() method is being called in HBaseRPC.Server.call() with the call method name. So it looks like that's how they're getting populated. – As an aside it looks like rpcQueueTIme and rpcProcessingTime are incremented twice there is debug logging is enabled – I'll try to test this out as well a bit later.