Brody Ekberg, I have walking onions, garlic, and comfrey interplanted among my fruit and nut trees. I usually plant things about 12"-18" away from the tree seedlings. My walking onions tend to "walk" that far on their own, so I'm just sticking with what they naturally do. My comfrey is also very aggressive, but it handles hard pruning very well (4-5 times a year). I chop and drop it intentionally to use as mulch around the saplings.
Without any specific science to back it up, I aim for as much diversity as possible among my fruit and nut trees. So in addition to the alliums and comfrey, I interplant with perennial medicinal or beneficial herbs and flowers. This includes yarrow, wormwood, echinacea, rhubarb, strawberries, raspberries, blackberries, etc. These smaller plants do sometimes crowd the saplings, but by the second year, those saplings were firmly established. Now I'm more worried about the little guys getting shaded out.