In 4.x, is it a best practice to customize the default template or duplicate the default template and customize that? I would like to future proof my customizations as much as possible!
It's usually best to duplicate the basic template just for your own sake, but I don't think it's necessary; I did the upgrade from 4.0.1 to 4.0.2 and nothing was overwritten during the process; CS Cart developed the new theme system so that theme styles can be completely portable moving forward, so regardless of which template you edit you should be safe!