"I guess they're just doing what they can to manage some of the risk by setting certain limits on who can participate."
That's exactly what it is. A few deserving people may be declined unfortunately. Philmont could potentially be liable if they allowed someone on the trail who is overweight and has trouble, despite the waivers I would imagine advisors have to sign.
I know smoker's would have similar problems, and that's why they'll check your blood pressure at the health lodge.