Definitely 12 inches on top of the tree roots could do serious damage, up to and including smothering the roots and killing the trees! I have never added more than an inch or two under trees and I keep it to leaf mold or light soil mixes with lots of peat and compost in them. Water - or lack thereof - is as much of a problem as anything under trees so I lay soaker hoses to make watering efficient and plant near the hoses. I think you are likely going to do less damage digging planting holes than you would if you smothered the roots with 12 inches of soil. My backyard garden is primarily under old white pines, a juvenile red oak and a mature green ash. I let the pine needles, ash and oak leaves stay where they fall in the garden and mulch the leaves that fall on the lawn area and add the chopped leaves to the garden beds. That's enough to feed the plants and soil without smothering the trees. Everything grows great there. When I started the garden area under the oak, after I removed the grass I did add about 1-1 1/2 inches of very light soil mix but that was all. I was very careful to keep it away from the trunk flare (where the trunk meets the ground...) as this area is where trees are very vulnerable to damage.