The geotags that are written in the image exif are acquired from the GNSS receiver on the drone. It records where the camera was located when the image was acquired. PIX4Dmapper uses this data, along with the orientation of the camera, to help establish the external camera parameters. Essentially it uses the exif data to establish the spatial orientation. If the camera happens to be at nadir (straight down) then the horizontal coordinates captured in the exif will represent horizontal coordinates of what is at the center of the image.
But its best to understand that PIX4Dmapper will use the external camera parameters along with the internal parameters (focal length and image size) to generate keypoints and to triangulate the positions of those keypoints. This is the basis for photogrammetry. It will assign x, y, and z values for all of those points. To sum this up, PIX4Dmapper uses the image coordinates to help establish the spatial orientation of the image.