Dirtdorphins, you are quite the excellent speller! And you have an enviable assortment of material.
As this is my first post in the Rock garden forum, I'll introduce myself as a 25 year NARGS member. I grow alpines mostly in troughs and pots. I love to grow from seed, and consider myself a mad propagator. But I am still not nearly as accomplished as Lori (growitall).
Regarding wood, is it the wood and the fungi that break it down that is "bad" for alpines, or the conditions that decaying wood thrives in?
Probably some of both, but fungi that invade and break down dead wood tend not to be the pathogens that are directly deleterious to alpine growth. Still, both wood and wood decay fungi help provide the environment for the "bad" fungi to prosper, so we are splitting hairs here. And as was said, while the use of wood might be okay or even good in the high desert like conditions of Utah (for example), it would ultimately prove itself unusable as a major component in alpine gardens of the much wetter climes of the Pacific Northwest or the eastern seaboard, and in places where summer humidity is oppressive. Growing alpines necessitates the mimicking of the environment they want, and that will change depending on the basic climates of the geographic areas.