I dunno, I think this is one of those things that while it's not technically required to ask permission, it would be a nice and neighborly thing to do. I don't agree with the "my yard, my berries" thought, because you didn't buy the bush, you didn't plant the bush, you're not watering/fertilizing/etc. so no, it's not your blackberry bush. I guess I'm thinking a heads up to your neighbor that the bushes were growing through the fence and producing tons of berries would have been polite, because he may have wanted to prune them back if he realized that so much of the plant's productivity was happening on the other side of the fence.
I think he was being very polite by giving you permission to enjoy the berries, and I'm not really sure why it rubbed you the wrong way. Maybe he was just telling you that in case you thought the berries were poisonous and hadn't been eating them, and he didn't want to see them wasted?