A drawing would help clarify what you're talking about doing, but it sounds like you're making a sandwich out of 2 steel plates, bolted together with rubber "jam" in the middle, to use as the main beam of your gantry. I don't think that will be as rigid as a solid assembly, although by using bolts you won't risk distorting it with the welding process. Is the point of this to make a quieter machine? If your goal is rigidity, a box beam would be better than the sandwich, since it gives more protection against torsion, the tendency of the beam to twist when confronted by cutting forces leveraged by the extension of the Z axis. If this is a fixed gantry design, weight isn't a problem, so the bigger and heavier the beam is, the better.
People here have experimented with putting sand into the hollow spaces of their machines in hopes of deadening vibrations; they report some success, but loose sand doesn't seem to work as well as sand consolidated with some kind of adhesive and packed in firmly.