100% N1
 

What exactly does 100% N1 correspond to, since most of the time, at T/O-thrust, you see reference thrust settings just over??

You're right in suspecting that it is not very meaningful.

Early in the design process they set a nominal design point for the fan (3900 rpm for an RB211-22/524).

This allows instruments to be standardised with % values, but the actual limits in % terms can vary even among variants of the same engine (e.g. RB211-535c to -535E4)