Like all of our tools you can manually edit the geometry inside the groups to exactly how you need it using traditional SketchUp functions and tools. However, I would recommend only doing manual edits once you no longer need to change any of the parameters in the Slab Tool dialogue or using either the Penetration, Void or Recess Tools , if you can help it, otherwise any manual edit will be removed.
It shouldn't have any affect on the takeoff as long as the slab is whole and there is no extra geometry in the group. You can check to see if it'll estimate by double-clicking on the slab to go inside the group, then select the slab and check the Volume field in Entity Info. If the Volume field doesn't appear then there is an error and it won't estimate.