One more comment: maybe the ExTRA Team should update their rulesets. Performance Troubleshooter still finds a "bottleneck" if "LogicalDisk(*)Avg. Disk sec/Read" on the Log drive is below 5ms. Whereas you and MOM expect a value less than 20ms.
The same goes for "MSExchangeISRPC Operations/sec/user": ExTRA finds a "High user RPC activity" if this value is higher that 0.25 whereas you are talking about 0.75, 1.0 or higher. It might be also helpful to clarify by which "user count value" you divide "RPC Operations/sec". You don't mention it and "http://technet.microsoft.com/en-us/library/aa995886(EXCHG.80).aspx" gives us 3 possibilities. ExTRA takes "Active User Count" here - and I think its the best one.
Cheers,
Jan