The article is a bit confusing, and the photo with the station's name doesn't help,
The station names and place-name signs, when we see them written with Latin characters, are using romanization Hepburn rules since many decades ago, shinjuku stay shinjuku.
What is happening is that at the same time, the Ministry of Education had been officially teaching different romanisation rules to the Japanese, denominated Monbusho system, which is slightly different with some latin syllables, like si (shi in Herpburn) or ti (chi in Herpburn), but now they are officially going to step towards Herpburn rules, the same as those used in the place-name signs when are written with Latin characters.
The station names and place-name signs, when we see them written with Latin characters, are using romanization Hepburn rules since many decades ago, shinjuku stay shinjuku.
What is happening is that at the same time, the Ministry of Education had been officially teaching different romanisation rules to the Japanese, denominated Monbusho system, which is slightly different with some latin syllables, like si (shi in Herpburn) or ti (chi in Herpburn), but now they are officially going to step towards Herpburn rules, the same as those used in the place-name signs when are written with Latin characters.