When you make a Mesh fill image, there is nothing in my opinion saying you can not make a layer, that is not mesh fill. And place that layer on the top.
For example this image of Dzen, which is a good one, to put freckles, let say dots on the face, you can very easy make a new separate layer, with dots. Then use the Transparancy tool and make the dots very transparant.
If dots would´nt be possible with Mesh Fill, then make the dots as I suggested. Or any other way.
For example if you are doing an illustration for let say a magazine (which I do quite a lot), and you like to use Mesh fill. But it HAS to have freckles. If impossible with Mesh fill, then I would use the way I suggested. Or another way, maybe even bring it into Photo-Paint and Paint the freckles. I would in other words, use any tool to make the dots. I wouldnt be a slave under the Mesh Fill Tool. I would only try to do the image as descided.