I'm not sure about the rest of the country, but up here in New Hampshire, Vermont, and Maine there is a growing interest in trail courses. Last fall I got an email asking for certification of a 50-mile trail course that spanned the border between Massachusetts and Vermont. Oh yeah, and the folks organizing the race were also asking me to do the measuring.
This was a point to point course over some pretty rough terrain and I must say that I was relieved when I got your reply to my email saying that we cannot certify trail courses. As it turned out, this particular course could not have been measured, because bicycles were not permitted on the trail.
I have measured and certified road courses that have incorporated sections of hard-packed well defined trails. I'm comfortable that these can be reliably laid out year after year. I guess the difference is that the start and finish for these were off trail and located relative to fixed landmarks allowing the overall length to be validated.
I'm not sure that documenting the course on a map is a big issue, since many of the maps for currently certified road courses carry the notation "not to scale." Of course, marking splits on a trail is a problem. Some of the sections that I've measured, such as in conservation areas, do not allow any type of permanent marking. (I place wired flags (from Home Depot) at splits during my first ride and retrieve them on my second ride.)
Perhaps the answer to the question lies in the improving technology of GPS and establishing a separate category for trail courses, with the coordinates for start/finish recorded on the certificate. Race organizers could still maintain and reward course records, but these would not be eligible for national recognition.