I think you misinterpret the 'rare places' section.
As stated there: Everything seperated by a ' - ' is considered as an individual place.
That means: This tool expects routes to be named like City A - City B - City C. Now, the combination of cities A, B and C will be the route (which appears at 'Most frequent routes') and the single cities will appear each 1x at 'Most frequent places' and all of them 1x at 'Rare places'.
In your case, the 'Rare places' section is useless, as you don't state single places, only complete routes. The table shows kind of the bottom of the 'Most frequent places' table - and at some point, when doing the route again and again, it's not considered 'rare' anymore.