I know ATS routes are made up of waypoints, but what are Significant Points used for? Is there a difference, or are they really just two names for the same thing?
According to ICAO PANS-ATM (Doc 4444) 16th Edition,
Waypoint is a type of significant point.
Mentioned in Chapter 1 - Definition as
Significant point :- A specified geographical location used in defining an ATS route or the flight path of an aircraft and for other navigation and ATS purposes. Note.— There are three categories of significant points: ground-based navigation aid, intersection and waypoint. In the context of this definition, intersection is a significant point expressed as radials, bearings and/or distances from ground-based navigation aids.
Waypoint is defined as a specified geographical location used to define an area navigation route or the flight path of an aircraft employing area navigation.
So in short waypoint is a significant point used to define an area navigation route or the flight path of an aircraft employing area navigation