Are "intelligent agents" supernatural?

We have recently had the jaw dropping experience of Joe Carter stating that Forensic Science does not use “methodological naturalism” because the mind is a “supernatural” entity. However, this kind of reasoning is used by other ID advocates. Francis Beckwith has written:

ID theorists maintain that contemporary science's repudiation of intelligent agency as a legitimate category of explanation is not the result of carefully assessing ID's arguments and finding them wanting, but rather, it is the result of an a priori philosophical commitment to methodological naturalism (MN), (n4) an epistemological point of view that entails ontological materialism (OM),(n5) but which ID proponents contend is not a necessary condition for the practice of science.(n6) (p. 457, "Science and Religion Twenty Years after McLean v. Arkansas: Evolution, Public Education, and the New Challenge of Intelligent Design." Harvard Journal of Law & Public Policy 26.2 (Spring 2003: 455-499)

To paraphrase Mr. Babbage, I cannot apprehend the confusion of mind that would result in the above statement. What do ID “theorists” think that forensic science, anthropology and archeology do if not address intelligent agency as a legitimate category of explanation? Last time I looked, forensic science, anthropology and archeology were all standard science fields using “methodological naturalism”. We’ve looked for intelligent agency in the origin of the HIV virus (and come up negative). Maybe ID “theorists” object to the fact that they deal with design by human intelligence, but science also deals with design by non-human intelligent agents, as I noted in my comment on the ability to determine that certain stone piles in rainforests were chimpanzee hammer stones, and the investigation of creative tool-making by Pacific Island ravens (Bird Brain will never mean the same thing again). Again they might object that the intelligent agents were all contemporary, and we could observe them, but we can also discern design by long vanished non-human intelligent agents, australopithecines (and Homo erectus, but they are human, although not modern).

As Francis Beckwith visits this blog, and had to discuss this issue with ID “theorists” to write the above paragraph, perhaps he could be so kind as to inform us what ID “theorists” mean by “intelligent agency” that it excludes humans, australopithecines, chimpanzees and Pacific Island Ravens.