The 3rd (freight) track, if my viewing of project documents and Google maps is correct, runs from a Metrolink connection near Claremont to the Miller brewery in Irwindale. Keeping a separate freight track in the r/w is done often enough, and avoids a lot of complications where light and heavy rail have to share a route to maintain freight service. Sacramento did the same thing in several places. For that matter, a lot of LA's Blue Line (or whatever they call it now, downtown to Long Beach) essentially shares r/w with freight tracks but no physical connection. San Diego is somewhat unusual in that freight and light rail share the same tracks (time-separated rather than physically separated) on lines to Tijuana and El Cajon, and Oceanside to Escondido.

Obviously, light rail trains don't meet FRA standards for unrestricted sharing of track with freight operations. You need heavier equipment, like SMART's, to do that.