GCP's outside processing area

If I have a project with GCP's and I draw a processing area that excludes those GCP's, are they still used in georeferencing or are they exiled?

I ask because we have a large 10 mile project where the point cloud becomes a massive file size, but we're capturing more data than needed. The actual design falls inside the boundaries of the GCP's like it should. But I would like to take the design file and export a KML boundary to import into Pix4D to use as a processing area. This will probably cut our point cloud size in half. However the processing area will now be inside the GCP boundary.

Will the georeferencing be affected? Does it depend on when the processing area is imported, say either before or after step 1?

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