@jmenze Ok. I think I found some something.
The values below are all used for the initial positions for the scapula and clavicula.
ShoulderArm.ModelParameters.Clavicula.NeutralPositionOnPelvis_pos
ShoulderArm.ModelParameters.Clavicula.Clavicula_Axes
ShoulderArm.ModelParameters.Scapula.NeutralPositionOnPelvis_pos
ShoulderArm.ModelParameters.Scapula.Scapula_Axes
But they are also used to calculate a length of the 'conoid ligament'.
See: "Body\AAUHuman\Arm\ScapulaConoideumDriver.any"
The ligament acts as a kinematic driver on the scapula. Scapula position is given by the AC joint (3DOF), it's contact with the trunk ellipsoid (2 DOF), and the a constant conoid ligament length (1 DOF).
So when you changed scapula value "NeutralPositionOnPelvis_pos", you also made the conoid ligament much longer. This caused the scapula to fall off its trunk surface.

You can see the little conoid ligament (selected) is too long.
How could I correct the initial position of the scapula instead? The problem is that its really sitting inside the rip cage
Maybe I should ask why you care that the initial position of the scapula looks a bit od?
If you want to prevent the scapula from penetrating the thorax we should change the surface upon which the scapula slides. Or move the contact points under scapula a little deeper. After doing this we should update the values below so we get the right neutral scapula position.
ShoulderArm.ModelParameters.Clavicula.NeutralPositionOnPelvis_pos
ShoulderArm.ModelParameters.Clavicula.Clavicula_Axes
ShoulderArm.ModelParameters.Scapula.NeutralPositionOnPelvis_pos
ShoulderArm.ModelParameters.Scapula.Scapula_Axes
I have a made a small model that does this. It removes the conoid driver and allow me to adjust the medial rotation of the scapula freely. If I knew the correct neutral scapula position, I can just read out new values for the variables above. With the variables update the conoid ligament length should automatically get the right length.
It is probably easier if I just show you. Do yo have time for meeting? Send me a email, and we can schedule a meeting.