It is very hard for me to explain it in english but i will try.
First of all you have to understand that there is no simple solution to this task. I understand that it is necessary to carry out the calculations for any two objects not only for simple objects like boxes or spheres. And the script also should calculate how much distance one object intersected with another object. For this I would use voxels.
Imagine that your object is recreated with boxes or spheres. Less size of the box or a sphere then the recreated object would be more like your one. But in programming you just need to use a point and a distnce to closest point but the distance should be the same for all points. For example crystal lattice of carbon is the most accurate voxel object.
But you don`t need to build the voxel model you can create an array with coordinates of this points.
I think you should use voxels. I would create virual voxel models and compare them.
