I followed the repro steps as you described (create 2 cubes, change settings, create 2 bushes) and both bushes were placed on top of the cubes. Could you provide a screenshot to help me understand what you’re seeing if this is not the same behavior happening on your end.
I was still unable to get a mesh to end up inside the cube when dragging it from the content browser, however I did notice that when the “End” key is pressed it does not place the bush on top of the cube as expected and I have submitted this report for further investigation (UE-7153).