It is clear that he holds that the main reason is that it was a pagan rite. He only added that he has another reason. The fact that the Gemara mentions Toeva as the confines of the Issur doesn’t necessarily put it in that category. The Rambam happens to say that many pagan rites were made up to satisfy lust, and therefore often contain very undesirable details. This might help put the Hagdara in perspective. The Chinuch mentions the two reasons for the Issur.
Regarding Uvchukoseihem, this is not the only place in the Torah where you will find this concept of a phrase that teaches us a Halacha put somewhere because of its Pshat connotation. We learn Davar Hanikna Miyad Leyad from a Pasuk that’s actually referring to Karka. Over here, the Pasuk says not to follow the nations. This in itself is a Halacha, that is related to Avoda Zara, and it is also put there as a Hakdama to the Parsha of Orayos. It has no practical purpose concerning Arayos.