I guess for me the issue is that the button is labeled "Explore" and when I enabled autocast, my expectation was that the ship would auto-explore. And by explore I mean "go out an explore the unexplored. The behavior that you're describing is one of the traditional roles of scouts, but not what I would classify as exploring -- more of a "gather intel" feature.
Future enhancement perhaps? A button on scouts that would toggle behavior between "gather intel" and "explore the unexplored"? As it stands now, I think the intel priority needs some balance so that it doesn't override the common sense. In a game yesterday, I was playing a 3-star map on single player with 2 other races. I had created a bunch of scouts, scouted my local system, then conquered my local system for all but 1 or 2 planet systems far out from the local star. I then created some new scouts (cause the old one were dead), researched the star jump tech, and then sent 5 scouts out to the two remaining systems. Those 5 scouts headed out to the other star systems and then immediately turned around to the home system to try and scout out the remaining 2 planets in the home system (which were on the far end of the home system away from the star). It's almost like you normally go out to the store to buy milk for your mother, but then one day you leave Michigan to drive to California to attend a conference. Once you get to California, your mom asks you to get milk for her. Instead of calling up a buddy and asking them to do it, you blow off the conference, drive home to Michigan and then go buy your mom milk.
My 2 cents.