A base-isolated building is not coupled to the ground in the same way as a standard building.
To quote from the following web site
" When a building is directly supported by the ground, the force of an earthquake is directly transmitted to the inside of the building. Providing a base isolation device between the building and the ground can minimize the level of earthquake force transmitted to the buildings by one-half to one-third. This system protects the building finish, furniture, utensils, electronic apparatus, building frames, etc. from the shock of an earthquake. Since the 1995 Great Hanshin Earthquake occurred, there has been renewed recognition of the usefulness of a base isolation structure system which serves to totally increase the safety of buildings against earthquakes."
Although this technique still needs work,
it does show great promise for large buildings
One way you might illustrate this with your shake table would be to attach one building with Velcro while placing the other table on a smooth surface, perhaps centered with four rubber bands tied to each corner to keep the building more or less centered.
Below are some pictures of a base-isolation demonstration. Two baby food jars are filled with colored water. One is attached to the shake table with Velcro, while the other sits on a smooth surface.
The water clearly sloshes up much higher in the jar that is attached firmly to the table.