I asked Williarob what he had been using for his Star Wars project:
Williarob said:
The best tool I found was Photoshop - If you save both versions as an image sequence you can record Photoshop doing it’s ‘Edit - Auto Align Layers’ thing as an action, and then run that on the whole folder as a batch, or maybe write a script to do it. It doesn’t always work, but that was the best tool I found for aligning sources.