However, I did make some suggestions on changing the skills and they way to level skills here, which kind of ties in with what you said:
I don’t think I explained it very well, but it essentially boils down to you get better at a task (gain xp and level related skills) by doing the task.
If we take rock to stone as an example, you would only be levelling up the ‘mass craft’ skill as it doesn’t really involve anything else, and only if you have that specific ‘crafter’ skill tree active on that character.