I do have some experience with Calypso so maybe I can help.
Let me see if I understand your problem, you have a sphere with a cylinder running through it, the cylinder is your primary datum with the center of the cylinder as the center of the sphere as well.
Assuming you are setting this up the easy way (with the center bore being aligned to +Z) and just scanning circles on the sphere and probably a helix for the ID cylinder I would use the cylinder for the alignment and as the X and Y origin, using the sphere itself as the Z origin. Since the object will obviously be true to itself in Z it's effect in position error is will be zero.
You are correct that the profile tolerance is effectively form + position error. (Runout functions in the same way.)
CMM's are bad at reporting profile. You'll have more luck simply outputting diameter, form error of the sphere, and position error of the larger sphere to the center diameter.