That is certainly one possible workflow where it might have limited application. The are a few others I think might benefit from something like geogig.
1. Quality Control. LIDAR gets edited during QC processes. An initial point cloud can be quite noisy, often to the point of being unusable. The point cloud is often edited either by automated algorithms (e.g., denoising), or manually by analysts, or some combination of the two. Being able to maintain that history would seem value to a QA process. For instance, reverting the results of some automated QC algorithm in order to apply another. Or merging the QC edits of different analysts.
2. Change detection. Being able to diff between two collections and create a "patch" would be another. For example, diffs with something like git can be be refined to ignore things like newlines, spaces, etc. A similar concept could be applied with something like geogig, where the diff refinement can be spatial in nature. So, two points within a certain threshold distance can be treated as equal. Therefore, the two point clouds in your example that cover the same area but the points aren't exactly the same could still be seen as "equivalent" within the diff threshold distance.
thanks
dan