I got the rocker covers with my flares.
They have a 1/8 inch indentation where the jack point cover would go, with the idea that you cut that out when you install them.

I have removed my jack point due to rust and I don't want to put them back to just start the process all over again.

So, how can I make this indentation smooth with the outside face and eliminate the risk of it popping out or cracking?

The can says "Kitty Hair" around here. FLAPS or any plastic shop will have some. Maybe even Walmart.

I would scuff the gel coat off the rocker first. I would also add some fiberglass gel to the kitty hair mix. It helps it flow better and fill voids. Then just sand smooth and finish with spot putty.

Here's what I would do. Grind the jell coat, either use a fibreglas reinforced filler or mix up some glas resin and mat it in. Grind it, fill it and sand it like anything else.