@Roel
I know how frustrating it is, I've been banging my head against it for quite some time, after good two years there are some aspects of 5D in Bonsai I haven't fully grasped, but I can happily and professionally use it for quantity take-off purposes, the full costing implementation will come later I'd guess.
1 – Where does this value come from, and how is it is used?
Schedule usage

This is more related to 4D, or time dimension than 5D (costing)
A resource can be assigned to a task and the duration of that task may depend on the number of resources assigned.
Task Duration = Work Quantity / (Number of Resources × Output per Resource)
"effort driven" example
Given:
Total Output Rate = 1 labor × 2 m²/hour = 2 m²/hour
Duration = 10 m² / 2 m² per hour = 5 hours
in this case by increasing the number of resources you reduce the duration of the task
as you might know not always is this possible since other factors can be at play, like "you can't put 9 women on giving birth to a baby in 1 month" , or when you need to wait for a number of days before the concrete cast is cured.
Using the above, once you have assigned some elements with their quantities to a task, the work quantity is calculated and it shows as Schedule Work (derived) from the assigned elements.
If the implementation of the above in Bonsai is not clear I can record something to explain it better
I have several questions and would be happy to get an explanation for one.
In the meantime I can continue with the rest of your list one at the time
In a way I am glad somebody posted specific questions on this topic, useful exercise