Why the miniscrew positions are yours to mark
The miniscrews of a MARPE appliance are placed into the palate, and the decision of where they go depends on what is beneath the mucosa: bone thickness, the position of the suture, the roots of the adjacent teeth, the nasal floor and the greater palatine vessels. That is a clinical judgement made from the CBCT, and it belongs with the treating clinician. The design service does not choose the anchor sites.
What the service does is make the marking precise and the consequences visible. The CBCT is aligned to the intraoral scan so that a position marked on the model corresponds to a known point in the imaging. The insertion axis and depth you specify are recorded with the position, and the guide slot in the appliance is built to that axis so that the miniscrew is inserted the way you planned it.
Where a marked position raises a question from the imaging, for instance thin bone at a paramedian site or proximity to a root, it is reported to you with the reason. The position is changed only when you change it.