Also, the whole context of Genesis 2 and on is very Mesopotamian (the Tigris and Euphrates, the word "Eden" itself), and Neolithic (farming, herding, Cain building a city). If that's right, and we assume the scientific timetable, then we can't really talk about "man" in the theological sense 40,000 years ago.
Theological "man" was likely created in the Mesopotamian Neolithic, ca. 7000-5000 B.C. Whatever happened before then was not part of man's story as laid out in Genesis.
It might be that man knew about these creatures. Breeding would not have succeeded between them. They may have died out prior to the Flood (their habitat might have been overrun by man who could vastly out-think them), thereby having no place on the Ark.