Apply Template does not copy the control points from the template. Why is that?
By default applying a template copies all settings from the template except for the actual source images and the control points (see Q2.13). Control points are never copied since they are specific to the source images. For example a control point could originally point to the corner of a building in the template project, but in another project the same coordinates may be in the middle of plain blue sky. In other words the control points are meaningless outside the context of the original images. If you just need a project to be stitched exactly like the template project, control points are not needed at all. Control points are only used by the optimizer to determine the best image parameters. The stitcher then only uses the image parameters, not the control points. Therefore it’s sufficient to apply the template and proceed straight to Create Panorama without running the optimizer.