I don't know any organizations that *prefer* for teams to plot UTMs in the abstract sense, but as a practical matter there are a few reasons at our events (Untamed et al) teams end up plotting points:
1) Plotting checkpoints on your map locks in your course, and we have often ordered our maps months in advance to save on costs, ensure they arrive and are appropriate, and honestly -- a lot of a wilderness course can be shifting in the final month leading up to a race, whether permit issues, weather concerns, or findings from a final course vetting. Ordering maps last minute is such a giant risk -- we did this for Apex in Switzerland (pre-plotted all our maps last minute, as an experiment) and I brought this giant roll of maps over with my luggage from the US just days before the race, but if that piece of luggage were to be lost, it would've been a disaster. We also had to rush ship the maps to me from the printer. Too many failure points for such a critical part of a big race! Not my preference! A lot of stress at the baggage area!
We've experienced all these above issues in the weeks leading up to a race before, and I'd rather have teams plot 25 points on a map than have to cancel, move, or otherwise change points that are plotted on all the maps already. Map printing can be $3000+ expense, not the sort of thing we do over casually.
2) Strategically giving UTMs for teams to plot while on the course can ensure that nobody scouts/tampers or otherwise gains an advantage from knowledge of the entire course. If you have a loop section on bike, followed by a loop section on foot, if people know the entire course they can cover a lot of ground on their bikes and potentially "cheat" on the section they will complete on foot later. In this contrived example, we would only give the foot CPs out after a team has completed the bike. Those foot CPs must be manually plotted by teams.
This being said, we have a new workflow we're trying for Untamed New England 2012 ( *** shameless plug:
http://www.UntamedNE.com now has preliminary race details posted and registration opens Oct 1st *** ) that will let us have pre-plotted maps for every map teams get. It involved us investing in our own giant laser printer (my office is 20% laser printer now!), negotiating a sponsorship with a waterproof paper company, and a few other logistical hurdles.
I don't relish plotting UTMs at a race, but I also know the barriers a race organization faces with this and so I'm very understanding.