Can you use the tools to get a raster closely aligned to a target raster then do a transformation, e.g., 1st order polynomial? I know you can't go the other way once you create a least one control link.
I don't quite understand the question. You can use the georeferencing tools in Pro or ArcMap (Georeferencing tools—ArcGIS Pro | ArcGIS Desktop ) to georeference imagery to another source. The auto-georeferencing tool is also very good to automate collection of control points against and existing image or image basemap. The tools enable you to collect and edit other control points and see the residual errors. You can set the order of the transform to be applied and then save the transform parameters with the image so that they are automatically applied when the image is added. The transforms can also be stacked.
Peter-- What I meant was can one use the rotate, scale and shift tools then fine tune with a transformation using control links?
Yes. You can rotate, scale and shift then add additional control points. The number of control points required will depend on the order of the transform you want to apply.
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