Optimize Alignment redoes the alignment based on the Sparse Cloud points in your project.
The advantage is that you can 'clean' the Sparse Cloud using the Gradual Selection tool. By getting rid of inaccurate points and redoing the alignment, you will have a more accurate alignment (and hopefully a better Dense Cloud). We haven't done any in-depth testing to see how much difference it actually makes, I hope to do that in the future. It'll be nice to know if it actually makes sense to go through the extra steps (on a Sparse Cloud with lots of points the gradual selection is quite slow).