0.96a still has the same expeditions with major factions from previous releases, so if player does not want to defend colonies personally, he still has every incentive to stack colonies (provided Hostile Activity is kept low enough) so that he does not need to rush home or wherever the raider fleets are to stop them.
I played colonies the same as before (no AI core use, only one item per colony), and the main difference is I do not have that first guaranteed pirate raid where I need rush for Orbital Station immediately (today, it is rush for Patrol HQ instead) and random pirate bases pop-up periodically for the -1/-10% later. Currently, the only threat to colonies in my game is expeditions from major factions.
The main reason to spread out colonies is the slipstream map (and more places in the fringe to get supplies and fuel), but that is not enough to not stack colonies in one or two systems to defend against expeditions. I still want at least two colonies per system (with Military Bases on every colony for more system fleet power) for defense against raiders, and since I am stuck with five colonies max, I get two systems to colonize.