Zephyr Pro and Aerial allows you to help with the points projection on the sparse point cloud.
This workflow, called bundle adjustment, is helpful to minimize the error of points projections.
Bundle adjustment is performed in auto by zephyr at the end of each merge and at the end of the structure from motion procedure but with Pro and Aerial version of Zephyr you can do it manually using control point both in 2D and 3D.
Have a look at our tutorial page : Tutorial Bundle Adjustment