WOW! There is a ton on this thread as well! I read through a lot of it but it is hard to remember every detail of the posts so I will say what I have to say
Personally, I feel like there does not need to be a spot in any skill tree for performing basic functions such as: crafting basic tools or weapons, trading, use of a compass, etc. A proficiency tree should be used for increasing how well you perform those basic actions. You can get benefits of increased functionality, hitting harder, crafting better, but only through use of that action whatever it may be. I am going to work on some charts and some more detailed information and post it at a later time.
@james P.S. If a dev could at least respond and give more detail on what main concept they want for skills and attributes and abilities, that could help aim my thoughts. There are so many ways to go about this and I am not sure randomly sharing my thoughts will help on this topic.