It's 2017, I'm using AD 17.0.11 and the problem is still here !
And, yes, I do have 3D bodies.
The only "solution" I've found is to change the mode with "R" key, to enter "Ignore obstacles" instead of "Avoid obstacles".
But then I can place a component totally inside another component.
There's no problem however for components that are "right angle".
Any suggestions?