Tim, I was wondering what happened to cause the base to crack - it's quite unusual. In our in-house testing, we found that a piece of 1/8" black neoprene rubber sheet worked just about as well in damping the sound as a thicker piece, without causing any problem. The version with the built-in seawater pump can make something of a racket if it is mounted directly on fiberglass decking with an empty space beneath it - the sound reverberates in the head compartment and can be annoying.
Another thing you can try (if you feel adventurous) is to go to a sheet metal fabrication shop and see if they have a scrap piece of 1/8" or 3/16" thick aluminum sheet. It can be an odd-shaped scrap, but you'll need a piece with a section 8" x 9" available to use. Set the base on the aluminum sheet and trace the outline of the base onto the aluminum sheet with a stylus, then cut it out with a fine-toothed (metal-cutting blade) band saw or sabre saw, so that you have the aluminum sheet the same size and shape as the bottom of the base. Note: in the back, where the "ears" are, cut it straight across; don't cut out the inset that lets the "ears" stick out - cut it straight across from the back of one ear to the back of the other ear. Mark and drill the mounting holes in it, in the same places as on the base. Deburr all the cut edges with a file; a sharp pen knife can be used to deburr the drilled holes (or you can hit each hole gently with a larger-sized drill, a few times on each side, to deburr the holes). Then replace your original rubber mat, set the aluminum piece on top of it, and set the toilet on top of that. Then bolt the whole works down. That should provide adequate suppport so that the base won't crack - just an idea.