Ah, that is exactly the point. He has no rational basis to recognize Christ in the breaking of the bread, but not face to face. This points to Christ’s presence in the broken bread, i.e. His eucharistic presence.
He has Jesus sitting right in front of him and he also sees Him in the bread? Two places at the same time? The disciple was having trouble with he resurrection just like the other disciples did until they saw the empty tomb. It was the fact that the rabbi was sitting in front of them and when He celebrated the sacramental brotherhood feast, the breaking of bread, they recognized him as the resurrected Lord. There was no magic to it, it was just the ancient rite of the brotherhood that united them around the rabbi. Look at John 17, “that they may be one as We are one You in me and I in them”. Did Jesus eat the body of the Father? The bread was the symbol of unity (many grains making up the one bread) as well as the eschatological testament (will) they participate in His inheritance, the kingdom.