PAA you find many times machlokes in Metzius and the din one way or the other (how long is Bein Hashmashos, was the Beis Hamikdash mekudash latid and many health machlokes which are paskened) also the Chofetz Chaim is notorious for quoting the Zohar and many Midrashim in the Shmiras Halashon, Machne Yisrael and his other works and paskening from this (its interesting that in the MB he only quotes a Zohar when it was previously quoted by the Nose Kellim but then again that is how the MB differs from his other Sefarim).
Sof Davar I think this is a root difference between Chasidim and Mitnagdim in how important a role does Hashkafa plays and you see this also in the way they live and write their Teshuvos. For example in the Divrey Yoel he argues on Rav moshe regarding the Mechitzah and one of his main arguments is that the Divrey Chaim said that this is that way Klal Yisrael are Noheg (I don’t think Rav Moshe was phased by this), he was also Cholek on the Kneses Hagdolah that the MB brings in Hilchos Tefilin regarding the Zohar including with it the Kisvey Ari not like Rav Moshe. This is also why the Chsam Sofer held like that (he way Hungarian and very close to Chasidim, Rav adler and the Haflah were his Rebbeim). The Chofetz Chaim was his own personality.