Manual Trigger Collision Detection via Script

Hi,
I am working with a generative grammar that replaces placeholder prefabs with new objects, some of witch have again placeholder objects etc. First I was working on a grid, but now I want to loosen the script from a fixed grid. My problem now is how to avoid generating overlapping structures, witch I don't want to have. I thought about after instantiating a new prefab, I could just test if it collides with any existing prefab it shouldn't collide with, and if it does, I delete it and try another one. But as it seems there is no way to manually ask for a collision detection in a C# script.
I found workarounds with Physics.SphereCast or Physics.BoxCast and such, but I would appreciate if I don't have to approximate all my models.
Is there any way one could achieve a manual collision detection in C#?
Thanks you for your help.

 

As 00jknight pointed out on reddit: Physics.ComputePenetration does exactly that. I still have to iterate over all my GameObjects to get their colliders, but I'll write a custom function for that.
NOTE: Physics.ComputePenetration is only available in Unity 5.6