I do agree that it needs a fix of some sort. I can see one problem with the proposed solution - if you have several backpacks open the game will need to somehow know which container to move the item to.
Maybe CTRL click to mark multiples like in windows, allowing you to click the items and drag just once would be a workable solution?
In regards to usability - if you put your crafting tools (hammer, etc) in a bag you can open that bag and then change inventory tab to Ingredients. That way you can hoard all ingredients straight in the inventory and still do crafting easily.
In regards to items you keep simply because of your hoarding tendencies - right click and send to Homestead puts them in your Homestead chest for safekeeping.