I think "functional reliability" of > 0.95 means that a failure of 1 in 20 to detonate could be acceptable, whereas "safety reliability" of > whatever refers to the chance of improper arming of a weapon. False negative vs. false positive, if you will.

While both could be catastrophic under some circumstances, it seems reasonable that you would expect "safety reliability" to be much higher because it's tested more often. Near the end of the document it talks about how safety reliability should be very high.