The fares are all distance-based and based on the most direct routing, so this sort of thing would happen in many instances where you are taking the long way around a more direct route. For example, you could take the Marunouchi Line from Shinjuku-sanchome to Ikebukuro for less than it would cost to go from a "closer" station to Ikebukuro, because the system assumes you are using the much more direct Fukutoshin Line.

Speaking of fare oddities on Metro, how about the segment between Kita-Senju and Ayase on the north end of the Chiyoda Line? It can be treated as either a Tokyo Metro segment or as a JR segment for pricing purposes depending on where you go at either end. If you start at Ayase (or come in from the Joban Line), go to Kita-Senju and immediately change to the Joban rapid line to Ueno, it gets counted as a JR segment, but if you come in from Kita-Ayase and change to Joban rapid at Kita-Senju, it gets counted as a Metro segment along with the Kita-Ayase to Ayase sector.

A similar rule applies between Shirokane-Takanawa and Meguro because the system has no way to tell whether you took the Metro Namboku Line or the Toei Mita Line. Instead, the system decides which train you probably took based on the routing at either end of the trip. (I think it also assumes you took Metro if you are only riding between Shirokane-Takanawa and Meguro, because Metro is cheaper.)