Messed around a bit more with the above fort, extended the z-level drop a bit, set a carpenter up down there with a 1 tile wood stockpile directly under the drop, and have had him making beds on repeat so he'd have to be accessing the pile as often as poss, he's managed to avoid getting hit up to now but i guess it's only a matter of time before he'll be in the wrong place at the wrong time, after all the carpenter has to be lucky every time he wants to make a bed, the flying pile of lumber only has to be lucky once, then it's bye bye carpenter.
With wood i guess you aren't chopping trees all the time, so there comes a point where the cart's not being filled until i designate more trees to be felled, so i guess locking the stockpile behind a door for a little while when you're logging works or other similar ways of making it inaccessible for a time, with your quarry and stone though i assume your gonna be digging a lot more than i'll be chopping trees, and your carts are gonna be dropping much more frequently, could you put a hatch perhaps at some stage of the drop that you link with a lever so you are choosing when stuff falls?
Maybe a more elaborate pressure plate system that blocks the minecart or the drop at some point triggered when your crafters head over to pick up an item so when they are stood on the stockpile there's no way for stuff to drop on them, then opens up again when they leave? (i don't know if that's possible, i've never really played with pressure plates but it sounds sort of reasonable i think)