If any of the lower edges of any of the sides are lower than your bottom glass, you absolutely will have a failure. Your sketch sort of shows this. The weight of your water column will rest entirely on the bottom piece, shearing the silicone bead. The side pieces mearly hold the water "in". The bottom holds the water "up". Silicone has great adhesive strength, but almost zero shear strength. They don't build bridges with silicone 
As the others have suggested, styrofoam will "fix" the problem. It will compress wherever the sides are lower than the bottom piece. The bottom itself has a large surface area and the styrofoam will compress and distribute the weight.
Good luck!
As the others have suggested, styrofoam will "fix" the problem. It will compress wherever the sides are lower than the bottom piece. The bottom itself has a large surface area and the styrofoam will compress and distribute the weight.
Good luck!