I have been to Philmont, but it was a tour, not a trek. In September Philmont runs a fly fishing trip for Scouters from various Councils, and I got to go last year. I (and my Scout Executive) drove from Albuquerque through Santa Fe and Taos to Philmont. We tossed our bags into a cabin and then went off site for a bison barbecue with adult beverages, and got a tour of a local museum. Great stuff! The next two days were essentially a tour. We weren't actually particularly interested in fly fishing (we did about 3 hours worth), so our guide drove us all over about 1/2 of Philmont. We saw wild turkeys, wild burros, elk, antelope, deer, bison, and T-Rex tracks. It really makes me want to get some Scouts up there for a trek before I get too old to make one.
The nice thing about Canoe Canada, BTW, is that they’ll provide as much or as little outfitting as you need, and they are used to working with Scout groups. If you need everything but the clothes on your back, they can do that. If (like me and my brothers) you bring all your own gear and food and all you need are permits and canoes, they can do that, and adjust pricing accordingly. If you want a great trip, and want the wind at your back coming back into base, check them out at www.canoecanada.com.