I'm so happy to know you're getting a lot out of Pilatesology -- I see your great comments and I know you are just as curious as I am to know everything about Pilates :).
You are correct in your observation that there is not very much instruction on the breath in some schools but like you said, It is very specific in Return to Life. So why the difference?
I have asked this question myself many times and here's the answers I received (these are notes from my memory, not their exact words):
Romana - there are some exercises where squeezing all the air out of the lungs is the goal or where breathing in general is instructed specifically. For ex: Double Leg Stretch, Coordination and Down Stretch on the Reformer, Snake/Twist on the Reformer, Breath-i-cizer etc... Romana often instructed the breath when she was teaching but it wasn't as obvious as the all capital letters that Joe uses in RtL and, sometimes she would switch the breathing rhythm away from what you were used to just to mix things up. When asked how we should breathe, she talked about getting all the air out of the lungs and if we do that it's not necessary to focus on the breath all the time. Just use your common sense and make sure you are not holding your breath.
Jay Grimes - gives the example of teaching a child how to swing on a playground. You don't break down the movement by saying 'kick your legs, lean back, lean forward..." you just give them a push and they figure it out. He definitely instructs breathing on certain exercises but it's very simple -- breathe in... now wring all the air out as you twist...
Kathy Grant - in my lessons with Kathy she taught breathing and some of it was her own invention like the hissing cat and methods you can see Sarita Allen and Blossom Leilani Crawford teach in their videos. However she did not breathing as specifically as it is written in RtL.
Ron Fletcher - I took several workshops with Ron and he taught his own breathing method in them. It is very specific and not what Joe writes in RtL but I found it effective for connecting to my powerhouse and concentration.
I'm sure you've seen my mat workouts that follow RtL and in those I instruct the breath as closely to Joe's text as possible. I loved doing that project and felt like I learned a lot about how our breathing changes our movement. I don't think there's anything wrong with cueing each movement with the breathing but if we do that, it can become a lot for our clients to absorb and at some point they need to be able to do it themselves in a natural way.
I hope this long explanation was helpful, I have been wanting to do a workshop or series about breathing for a long time so I will add it to our list for upcoming classes!