I think Auto-Magic Coat has a lot of value - not just what it actually does in the metagame, but the psychological aspect it has on people by looking at it.
Okay, sure, AMC might be horrible at actually blocking the secondary - it might be the most amazing thing the world has ever seen at deterring secondary moves. We're probably not going to know until sometime late-post playtesting. By the time general consensus actually forms a solid opinion of how well AMC works, people are going to come up, see AMC and start thinking, "Woah. They made an ability that's designed to block secondary moves."
That's going to have a huge impact on the way people think about certain decisions. Especially in team-building and the early game. The idea that Auto-Magic Coat (particularly) is there - and that the Pokemon it's on will be one of the most popular for the duration of playtesting - is going to affect how they consider using the secondary.
Think of it like Fidgit with Persistent. When it initially came out, there were quite a lot of Trick Room teams and the like. Eventually it tapered down, but early on a lot of people fixated on Persistent's effect and it translated into the metagame. Since one of our goals is to see what would happen in a metagame that encourages less of a focus on the secondary, I think that, just by implying that this Pokemon can destroy the use of the secondary (regardless of whether or not it actually does), we can go a long ways towards accomplishing that.
Of course, I believe AMC can be useful and have long-term benefits... as well as that it could do really well paired with Guts and the like. I'm just saying, if AMC does great or poor, it's still going to affect how people look at using the secondary... at the very least for the two weeks we're going to be intensely studyng this.