Any skill test affected by magic would include anything that Stainless Steel Devil Rat mentioned; threshold changes, limit changes, DV changes, any part of the calculation. Then BGC is applied as a penalty to the dice pool. What Kiirnodel mentioned is also accurate. There's no rule about any powers being "treated like foci", it's just a binary of "if magic is helping you do this thing, you get the penalty".
I'm not sure what you're confused about. Yes, the penalties really do theoretically go up that high and down that low. The book explains how, once you get to around -16, there starts being effects that are dangerous and can be felt by anyone, not just mundanes. You can't just compare penalties to wound penalties as for whether or not they are reasonable. Being totally in the dark is as much as being "on the brink of death", as you put it, but it really does penalize you at -6.
Also there's no rule about acclimation automatically happening, unless you think Forbidden Arcana having a random buddhist quality off-handedly mention the back half of what would be a major rule wasn't a mistake. (I'm sure it was.)
Adepts unfortunately do get completely stomped by background count as it reaches higher amounts in the current rules.