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The ROS navigation stack is based on move_base and uses global and local planners and costmaps . I dont know much about the diff_drive package you linked but what I can see from description is that it is a "lighter-weight" solution than the ROS controller framework and uses actionlib and PID to calculate velocities. Also I see that is subscribes to move_base_simple/goal just to grab the goal given via the RViz 2D Nav goal plugin.
As for the waypoint navigation, you can write your own node that can send multiple waypoints using SimpleActionClient from actionlib. Also there are some packages like the follow_waypoints that already have some implementation of waypoint navigation.
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