Thanks for the feedback! A lot of this makes sense / we’ve heard it before.
One thing I can tell you right now is that you can remove the plot sign when you’re done configuring it, the plot remembers.
The purpose of the hoppers is simple close-range movement of items. Use case number 1 would be filling and emptying machines that don’t require workers automatically , like the furnace. In the current version, you can also fill/empty packling stations with it and do the long-range transport with the packlings. Yes, it’s not well explained so far, true 
Some of these will be addressed in Alpha 4 already, like the forester zone having to expand or automated ways to get ingredients for crafting.
With the accidental deletion we’re not sure if it makes sense to add some interaction where you have to wait for a certain time, or just make a different tool, like a hammer, to delete stuff, will have to see.