Most crafting defaults to ground first, inventory second. Taking a step from ground stash will help.
As that's very useful elsewhere, I don't think changing that would be fair.
As for: "Are you sure you want to do that in here?" when in village or settlement and initiating something that the locals don't like, I do think it might limit the players/character's acts by guiding.
Similar to tabletop RPG gamemaster asking: " are you sure you want to enter the ominous cave... it IS full-moon" <<< guiding players with tone for something the character's wouldn't be aware about.
When leaving a village, especially if I previously saved in one, I do talk to an adult in the village, then attempt Trade, if they don't say I owe them for goods, I'm leaving. Alternatively, when you're holding unpaid items, there's inventory filter (tab) for unpaid. For easy dropping of all village goods.