One reason for this is the historical situation that a Shinkansen line was originally constructed as a new railway line additional to the regular railway line having been operated in parallel with it, and another reason is to avoid fare calculation from becoming complicated.
これは元来新幹線が並行在来線の別線増設として建設されたという歴史的経緯や、運賃計算の繁雑化を避けた事によるものである。