The shoulder joint should be supported since you mostly work on the back anyway. If you don't support it and lean into the joint, it can be a much stronger stretch. Also lying with an unsupported shoulder joint during the whole time you are working on the back in this position does not feel very comfortable.

Quite true. Large body + big knees on small back = bad combination. 

The knee is such a large surface that you won't be able to just lean on the erectors. You will catch other back muscles by default as well.

Several reasons:

1. In the Thai Massage system there is an energy line which sometimes moves to the edge or under the scapula. Lifting the scapula gives you better access.

2. For some techniques lifting the scapula gives you much better leverage. For example there are a couple of stretches in the side position where you lift the scapula to move the shoulder around.

3. There are different body types. Some people have a naturally loose scapula, and some people have a tight one. The purpose is not to separate the scapula from the back on every client, but to determine in which case a tight scapula goes along with upper back and shoulder problems. Those are the ones where you want to work on the scapula. 

4. For many people lifting and losening the scapula feels really good. Feeling good is a good enough reason for a technique in any massage system. Not every move has to have a specific therapeutic purpose. Like with all techniques, you are not following a mechanical sequence, but you build up a repertoire of techniques to choose from, and the art is to learn and intuitively know what works on whom. 

So there is no point in pulling scapulas on everyone indiscriminantly. However for some people and for some conditions it is a very useful technique. There is no specific rule which states on whom to use it. But with experience a therapist will feel when it makes sense to apply such a technique.

It is also one of those moves where I like to ask the client if it feels "good, bad, or neutral". Many times the client's answer to this question tells me if I am on the right track. I don't work so much based on some scientific reasoning, but rather what my intuition, my sense of touch, the client's feedback and reaction tell me.

After all, if you want to apply strictly anatomical reason to Thai Massage, the whole thing doesn't make much sense since its very basis is to work on energy flow in the body which is not recognized by the western model.

Interestingly enough, another student just posted her experience with scapula work. This is what she had to say:

"I did have to work with a partner whose shoulder blades were not stuck!  Working on the scapula is always a very beneficial to the client.  I work on so many people who carry all their stress on their shoulders and that tension just seems to trickle down and settle right in between the shoulder blades.  I did try the scapula techniques on my regular partner just to help her shoulders, and so I could see what the techniques feel like on a person with stuck scapulas.  I followed the advice given in the video, and kept my partner comfortable, and only did what her shoulders where capable of doing.  I did not force my fingers under her scapula, but just did what I could.  By the end of that practice session, my partner did comment how relaxing it felt just to have her shoulders manipulated that way."

Well, that's the thing about those energy lines. They are not exactly in one spot on everyone  in the same way. They can move, and that's why it is not a mechanical thing at all to work with them. It is something that you learn to feel intuitively. In some schools they paint the lines on one of the students to show their location. But those locations are only approximations, and not all the schools agree on them anyway.

The one  big issue I have with the typical Thai Massage energy line work is that it is really hard on the thumbs, especially when you are a small therapist with small hands. That might not be an issue for you since you are a big guy, but is it an issue for lots of therapists.

You might want to read an article which I wrote about his whole energy line subject. This will really clarify it for you:

Thai Massage And Traditional Sen Lines

I never tell clients to breathe in a particular way when I am doing spinal twists, and I have never heard a comment from anyone that it makes breathing harder for them. But then again I don't hold spinal twists. I generally rock into them and do them in a real fluid way while moving continuously. I think that would take care of any breathing issues.

I also do spinal twists mostly in the supine position. I really don't use the sitting position that much. I only use it when I want to do very specific therapeutic moves. But when I have the choice, I'd prefer to do a particular move in the supine position since this is just much more comfortable for the client.

The client's sacrum should rest on the balls of your feet. Your heels need to be pushed forward all the way so that the toes do not poke the back. The client should not feel your toes. They get bent down if your position is right. So your foot needs to be flexed in the ankle joint as much as possible. That reduces any toe pressure. In other words, your foot needs to be at a 90 degree angle to the floor. In this position there is no toe pressure on the client's back as long as the client's sacrum sits on the balls of your feet. Make sure to keep your toes completely relaxed and don't push with them. The pushing comes from the balls of your feet, not your toes.