“The emphasis his machon shilo places on Yerushalmi over bavli is his own chiddush”
He points out that the Rambam paskens in accordance with the Yerushalmi over the Bavli in a significant number of places. And the Rambam in the hakdama to Mishneh Torah explains that the halacha is derived from both talmudim as well as the other braisos, tosefta etc. He himself doesn’t blindly follow the Yerushalmi over the Bavli. When it seems to him that the Yerushalmi is correct (which might in certain circumstances be because he prefers the “Torah of Eretz Yisrael”) he will follow the Yerushalmi. He also points out that the Gra in Shnos Eliyahu often explains the Mishnah using only the Yerushalmi’s explanation without mentioning the Bavli’s.