Right, I forgot about the existence of containers at all, so I started using 'families' instead because I wanted pseudo-container behaviours.
When I put all the parts of the Deer container together, would I still have to do the On Start Layout event where I spawn and pin all the associated collision boxes?
Or after making the Deer-container, I just ctrl+drag to duplicate it throughout the layout and it'll be exactly the same?
You don't even need to spawn the hit boxes, that is done automagically due them being in same container. You only need to do the pinning, which I'd move into 'on deer created' event.
To summarize:
Only place instances of deer object in the layout, no hitboxes.
On deer created event, place hitboxes (to imagepoints of deer object) and pin them.