User blog comment:Hitsuji Mamoru/Servant Creation Room 2 : Guess of the Who/@comment-28209103-20170725160621/@comment-28209103-20170725203656

Stigmata by definition is mark of the lord, however this is closer to the mark that someone is one step closer to the Lord by receiving certain burden or trial as a way to purify them of their sins, just like how the cruxification of Jesus is the process needed for him to finally ascend.

Basically it's purification ritual that double with penance, in exchange the more penance one paid the higher level of mystery one can gain.

also for the NP part, actually, all of his skill is considered part of his Noble Phantasm, hence the EX. However ultimately he only have 2 NP he can utilize as "trump card" much like Jeanne, one of it is the NP listed here.