If the silicone is not cured before applying GS, then as the GS expands, it moves the silicone and shows through the glass. (and that is why I apply the silicone, so I wait the 24 hours for the cure.)
Another method I have used for small sections of great stuff is apply it straight to the glass, let it dry, then peel it off the glass and silicone it back on. This way you dont need to spread so much silicone and the glass stays clear where there is no foam.
Examples: