A mosaic is different, as the parts that will seam together and become part of the final image are all full signal. If you had one panel of the mosaic that had the issue you describe in your post, and the misalignment amount for that single panel is greater than the overlap you've set for your mosaic, you'd be out of luck with the mosaic. I suppose using PI or Photoshop you might be able to try to illuminate the darker part of the image to match the central portion, but as we have said you'd be dealing with a portion of the FOV that does not have the complete signal from both nights. That doesn't only result in a darker area, but less signal in your object.
Andy