If you can get it flat now, it will make sanding the clear coat easier.

Paint (unless thinned very heavily or applied very thickly indeed) has too much surface tension to fill dips. It just follows the contours of what’s beneath it. So if you leave those shiny pockets now, you’ll then just need to sand the clear back in that area to remove the matching dips in the clear, which probably means a couple of extra coats of clear to give you the depth to do so.

It’s always best to get each type of coat as flat as possible before applying the next type. You then know that any small pits in the next layers are just in that layer, so you should be able to sand down without sanding through.

In terms of looks, small pits as in your photo, won’t show up with flattened and then polished clear coat over the top, but you’ll need to add more coats to avoid risk of sand-through, which slows up the whole drying/curing process.