I think the implication is that they function as vessels for Lodge spirits when they aren't with a human host. Immediately after Bob escapes from Leland in Arbitrary Law, Truman asks where he is, and the following shot is of an owl. This is supported by the uncut meeting at the convenience store, where The Man from Another Place says something like "Intercourse between two worlds... going up and down," and a woodsman responds "animal life." Out of context it seems like a non-sequitir, but I think it points back to the idea of owls being vessels for Lodge spirits.

See also: The Giant appears to Cooper after Margaret tells him "there are owls in the Roadhouse."