Very long compilation time / Advanced physical optimization. Quartus Prime. Cyclone V

Yes the progress bar doesn't move a lot when the fitter is running. It isn't stalled but it's doing a lot of work. There isn't really a point in turning on the optimizations before you set up timing constraints imho.

If you have some parts of the design that don't have high timing requirements, or work on a slow clock, it can be a good idea to put your timing constraints now. By default the fitter will try to make everything as fast as possible (iirc the default clock frequency for the constraints when you haven't specified anything is 1GHz), and if you have slow signals putting correct timing constraints can help the fitter concentrate on other parts of the design and it *may* make your project compile faster. But this of course depends a lot on your actual design. At least define all your clock frequencies, and check in the timequest report that they have been interpreted correctly.

Do you have big combinatorial chains in your design, or anything that can make it hard for the fitter?