I have a little more information, if it helps. Before you get in range of the craft, it seems to treat the "heap" as a class A asteroid, so it may not have any snacks on it at all.
In rescue missions, I'm getting penalties for the stranded Kerbal starving. When I check the pod later, it has full snacks. It seems like for whatever reason, the Kerbal can't access snacks in an unloaded pod.
Is there any way to make the NFE Compatibility patch work for other mods atomic engines? Would it be as simple as just copying the info from the patch config into other mods' parts configs?