Linear progression while training that much running might be too much to ask for, unless he's very undertrained in the squat.
I would move to a more intuitive weight selection.
Currently training for a marathon, and still squatting, and this is basically what I've experienced. I was able to do 5-3-1 for a while and still make gains in both strength and endurance. Closer to the race, as my milage has increased I've gone onto a kind of auto regulating type of thing 2-3 times a week, and that seems to be ok, although obviously its slower progress on the lifting. But the training necessary to get through a 10 mile race, even with obstacles, is surely not going to completely halt your progress, as long as you're doing something consistently.