To paraphrase terribly what I've seen come through our internal forums over the last week, I finally found out that Auto-IPsec was designed in situations where a FortiManager was *not* used to centrally push out configuration changes concerning VPN settings to both tunnel endpoints.
The idea is, with a policy-based VPN (I haven't seen anything to prove it applies to interface-based VPNs as well), if a change is made on the responder side once a tunnel is already established, the change can be communicated to the initiator so that both will maintain their connection.
Does that help?