Rabbi Ouri Cherki suggests that the differing sources on who received the Torah from Moshe (the one in Eruvin and Avot 1:1, "Moshe received the Torah from Sinai and passed it to Yehoshua") point to the difference between the Written Torah and the Oral Torah (my translation):
"...The Oral Torah, known in Eruvin as "the order of teaching", is needed in order to inform us what we must do actively. Here comes the usage of the hermeneutics that clarify the Torah, whose result is the halacha and not the simple understanding of the text. This is a form of study that requires a set institution that decides what is right in unresolved cases, and this duty is implemented by the priests and elders.
In contrast, the Written Torah teaches the ethical direction that forms the base of the Torah, which is learned from the wording of the text, even if it is not halacha...the one in charge of passing on the ethics of the Torah is the king, who reads from the Torah "so that he may learn to revere the LORD his God" (Devarim 17:19), and even actively acts according to the Written Torah with regards to leading the state (Natziv on Devarim 24:16).
This is evident from our parsha: "Then Moses called Joshua and said to him...“Be strong and resolute, for it is you who shall go with this people into the land..." (Devarim 31:7). On the face of things, Yehoshua is only given military and state duties alone. Immediately afterwards it says: "Moses wrote down this Teaching and gave it to the priests, sons of Levi...and to all the elders of Israel." (ibid. 9). We find here that this matches with what is said in Eruvin, where it is evident that Yehoshua does not take part in the giving over of the Torah. However, immediately afterwards it says: "And Moses instructed them as follows: Every seventh year...you shall read this Teaching aloud in the presence of all Israel." (ibid. 10-11). It says תקרא (singular) and not תקראו (plural). Therefore, Moshe is speaking to Yehoshua specifically, who remained at Moshe's side, as the passer of the ethics of the Torah in the Hak'hel..."
We see, therefore, that according to Rabbi Cherki, Yehoshua was not mentioned in the "order of teaching" because he was not tasked with passing on the laws, but instead mentioned in Avot because he was tasked with the giving over of the ethics of the Torah.1
1 As for the anachronism between the "order of teaching" and the fact that Yehoshua was only chosen as leader at the end of Moshe's life, it's possible, in my opinion, that Yehoshua was always intended to be some sort of military leader/statesman - we see this from the fact that he was chosen by Moshe to fight the Amalekites, plus his tribe chose him to be their spy. Therefore, from the beginning he was already excluded from the role of potential law-giving elder.