I also would like to see this feature.
Right now by default in PoE -- you can pickup any item by clicking on it.
In settings, there is an option "only pickup items when highlite key is held down" -- which is by default ALT key.
This lets you click anywhere on the ground, attack mobs, open chests etc even if items are piled on top of it or covering the ground.
Simple fix for the bot is to have a checkbox asking the user "is loot on highlite key enabled?" if the user checks the box, then the bot will always hold down ALT, then left click an item, in order to loot it.
Otherwise, the bot will not have ALT held down -- and will never pickup an item on accident.
Problem solved, easy fix -- just change the loot function to {ALT down} + {LeftClick} then {ALT up}