This is a very good point.
As of right now the coding for the physics of DB3 is just about to begin.
If not in the first milestone, I am sure that at some point many of these features may be included.
One thing to note is that it may or may not be reasonable to have a pencil tool. This will depend mostly on how things are implemented. For instance, right now there are several methods being considered to program the walls:
1. Simple polygons, nothing else. The problem with this is that it discourages ant-bots. Also, this would make a pencil tool hard to code.
2. Polygons with subtraction polygons. This would be a good way to allow bots to "mine" or "eat" walls or objects. Hard to say right now if this would support a pencil tool.
3. Polygons with grids. Same as number 2 except that it would use a matrix to show where missing pieces are. Even harder to say how this would work out, but it does seem more likely to have pencil support.
Of course, there are probably several things I am forgetting here, and Nums will probably point these out, but this is basically how things are turning out right now.
