Yup. I have found the same with the junctions. Only the perfectly shiny track unfortunately is Protrack. If there was a rusty equivalent, it would work well with the track on the dirt ballast and less than perfect ties.Some of the ASCE Protrack types are quite good through can be a bit finicky about forming the procedural junction if the radius is too tight.
I believe there are also a couple of JR tracks that have been updated to Protrack type.