as you might see near the bottom catapult ... the arrow heads are sticking through walls, doors, etc...
wonder what it'll look like when the ballista is loaded... sticking through fortification?
The problem is that the arrows are 3 tiles long, but the dwarves treat it like it's only 1 tile long, so like you said, both the front and back of the arrow will stick out into things. I'd suppose a fix would be to make each one require 3 consecutive spaces in your storage piles - I wonder if that's currently even possible.
as long as some nut don't go around claiming an arrow defaced their wall or doors don't go around claiming it's held ajar and let the flood in