elvenpast: Alright, firstly toxicity is toxicity no matter how you gained it. Meaning, when the description to the skill talks about it, what is meant is your toxicity-bar and completey ignores HOW you filled that bar up. The only truly notable difference regarding the how is, that toxicity gained by decoction does not decrease until the effect wears of, while the toxicity gained by regular potions slowly wears off while being in effect.

So, to answer your actual questions:
1) Fast Metabolism is not entirely made redundant, because you can fall back faster to a safer toxicity lvl. If you have a tendency to overdose. But since you have put quiet some weight on the decoction abilities, I'd say that is not such a rarity? It's easier though to counteract the vitality-loss from poisoning yourself with the right potions...or food (the special skill "Gourmet" is rather useful in that regard) So, I would recommend choosing one or the other skill depending on your preferred combat style.
2) As mentioned above, toxicity-based perks don't care how you gained your toxicity unless it's specifically mentioned in the description. So, chuck a decoction and go nuts ;P
3) Again, same answer as 2. chuck a decoction and go nuts.