I realize it's too late for the original poster of the question, but for others with the same one, silicone won't take paint. Fill cracks with paintable caulk.
I think I'd use paintable silicone caulk to fill the gap. If it's quite wide you can use a piece of old panty hose to create a base inside the gap for the caulk so it doesn't drip right through to the underside of the counter. LOL, ask me how I know this can happen:)
Attach the sides of the patch cut to size from the stocking to the edges of the gap with super glue-be sure to position the patch so that it dips a little into the gap area. Doing that will create enough fill so that if you need to, you can sand any caulk that has raised above the surface of the area you plan to paint. Make sure you let the caulk cure for at least 48 hours in a warm dry room before trying to sand it.
A squeezable (eliminates the need to purchase a caulk gun if you don't have one already) tube of paintable caulk shouldn't cost you more than $3USD at a hardware store or your local favourite big box store.
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