Placing a bracket on a segmented scan
A bracket placed at the chair is judged against the tooth as it appears with cheeks retracted, saliva on the enamel and a bracket held in tweezers. Placed on a segmented scan, the same bracket is judged against the whole crown from any angle, with the long axis of the tooth drawn and the height measured rather than estimated. That is the whole argument for indirect bonding: the decision is made where it can be made well, and the tray only carries it to the mouth.
Placement follows your prescription. The slot is set to the height you use, measured from the incisal edge or cusp tip, and the bracket is angulated and rotated to the values of MBT, Roth or your own system. Where you place a bracket deliberately off prescription, for instance a higher slot on a tooth to be intruded, that is entered as your instruction and shown as such in the review.
The bracket geometry used matters for the tray. Where your laboratory's bracket system is available as a digital model, that geometry is used, so the tray's bracket seats match the real bracket base. Where it is not, a generic bracket of the same slot size is used and stated, and the tray seats are designed with the tolerance that requires.