Yeah, for resupply missions, agent deployments, and dropping off Marines, you have to stop the boat itself. For the latter two I think you might also have to do it at night (at least it forced me to do it at night), but for supply drops I'm pretty sure you can do it in the daytime.
Though once when I did a supply drop, the rubber raft somehow capsized as it deployed, so I ended up leaving the area while watching the two men in the raft row towards shore upside-down...
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