Mobs generally don't fall into holes unless they are pushed. In fact you would be semi-safe in a hole yourself, very useful when mining silver, not so great if one wolf pushes another in there with you.

Instead dig a trench around the whole base and take advantage of their reluctance to go into holes and their inability to climb steep angles.

For the workbenches, carry a small beam blueprint (or any other piece that's not a campfire or log bench) around and make sure it is buildable in every inch of your base. You can build if you stand in range and stretch the piece out of range, so keep it right at your feet to ensure there are no gaps anywhere. After you do that then you could replace a workbench with something else in the list if you want to, just make sure its in the exact same spot.