Terminology may vary, but what Skeinforge/ReplicatorG is calling "dangling edges" refers to one specific type of non-manifold geometry. It is the kind where an edge is shared by more than two faces. In other words, this is bad:
It is an infinitely thin shared edge, because even though each cube has a volume, they are joined in a way that is impossible in physical reality. Imagine if you were to perfectly line up two tables so that their corners touch in a similar way - would you have one table or two? You would still have two tables, of course. With this kind of non-manifold geometry it would be analogous to having the tables inseparably stuck together at the corner where they touch, even though they are only connected by a few molecules. A 3D printer doesn't know what to do with that.
Here is another example - infinitely small corners. Or if you prefer, "dangling vertices".
So what are your options? Well, you can either separate them:
Or you can create a very small area where the cubes touch that joins their volume:
3D-printable edge connection:
3D-printable corner connection:
Now that you understand the nature of the problem, your challenge will be coding into Python a new way of generating your geometry that is manifold. Have fun. :-)