Yes, it's a sign of truly being mature and in tune with the room when you know when it's time to take a break early (your are at a natural stopping point, the next chunk will take up to 80 minutes, etc) and when to let the natural flow of the room end before calling break (seriously, let them finish the speech then call the break). Know of a great story where the actor was four lines into "TO BE OR NOT TO BE", and the SM called break because it was 80 minutes since the last break - true, it was the "by the rules" thing to do - but sadly, not the most diplomatic.
I am big at talking with my cast up from on how I like to run rehearsal, and asking them how rigid do they want the breaks to be called. If they like the organic nature, I will let the work come to a natural pause, and if we just rehearsed 85 minutes, I will give them a 15 minute break. Often, actors can slip out and go to the bathroom, grab coffee during a call- and lord knows I slip out and use the restroom often during rehearsal - since during break I am being descended on. Other times, they are working with a director who is famous for wasting time, so they want the breaks called on time - to keep time moving. I full ultimately it is about making sure NO time is wasted, and everyone's needs are respected.
But, this is based on my management style, I am not sure every stage manager can get away with being organic and actor-centric as I tend to be. (This coming form someone who can keep three rehearsal rooms running for 8 hours straight - without any actor going into overtime . . . ) I would never advocate for any stage manager, young or seasoned, to not follow the rules of their contract, but there is a wall to honor the word and the spirit of the rule without looking like a tyrant.