Dear Rabbi Kornfeld,
We learn that when Rebbi Yossi said "veLo Amru leArev Chatzeros Ela Kedei sheLo Leshakach Toras Eruv min haTinokos", he's talking about the mishna on daf 90b; a case where shitufei muva'os is made, making eruv chatzeros unnecessary, and the halacha requiring eruvei chatzeros in this case was only decreed by the Rabanan so the halacha of eruv chatzeros would not be forgotten by the children.
Didn't we learn previously a case where shitufei meva'os was made, but they failed to make eruv chatzeros, and since it was asur to carry from the batim into the chatzer, the batim also made carrying in the mavuy asur; the batim being "blocked", or closed off by the chatzer, and therefore carrying items in the mavuy was also asur? Could you clarify this?
You are referring to the Gemara in Shabbos (130b-131a). In the conclusion of the Gemara there, the case under discussion is when they did not make a Shituf in the Mavoy, and nevertheless they are permitted to carry the objects of the Chatzeros into the Mavoy, as long as they did not make an Eruv between the houses and the Mavoy. The reason for this is that it is permissible to carry Chatzer-objects into a Mavoy (like Rebbi Shimon), and since there was no Eruv made between the houses and the Chatzer, there is no concern that there will be house-objects in the Chatzer (which are prohibited to be taken from the Chatzer into the Mavoy, since they came from the house). (See also the Gemara in Eruvin later, Daf 74a.)