Some people do wear double chamois for road riding. I would think that on a mtbike you'd catch the chamois on the nose of the saddle and get tangled. I personally wouldn't do it. Mtbiking isn't like road riding. You move around so much more that it doens't even compare. You're more likely to cause problems with two pads.

Your friend with the headaches. She needs to drink lots and lots of water. Has she really exerted at these altitudes before? Does she know she can tolerate it? Can she stay away from caffeine?