I believe the difference comes into play when the first project has JARs on it’s build path that you want the second one to see (export), then you can just add one project to another, export some jars and then the 2nd project will see the JARs, class files, and everything.
And yes MyEclipse will honor this when a web project depends on a Java project, you have options to package up or combine that Java project into the deployment of the web project. Also works for EARs.