Once you've bolted it and put the rubber on the bottom, fill the area around the bolt heads with silicone, it will form a barrier between the floor and the bolt head, not a very durable one if you drag it around alot, but should be ok for the times they'll be forced down towards the floor. And then the silicone just pulls out when you're deconstructing the unit.
Also if you put the bolts through and then silicone them while you're gluing the rubber to the bottom, it'll hold the bolts in place while you flip the board*.
*I actually have no experience with using silicone on wood. We use it on steel at work. It may or may not have the same abilities when used with wood.