Leave the epoxy alone. Stain the surrounding wood before you glue.
A couple guns ago I had a colerain barrel that ended up having a crooked breech plug tang. Didn't notice it till it was inlet. I had to file about 1/8" off of one side leaving of course a huge gap. I found a piece of wood, cut it to size and lined up the curl of the stock and the patch. I stained the patch and the stock, applied some crazy glue gel (Gorilla brand) and
hammered in my patch. I always taper the sides of my patch and my hole so I get a super tight fit as you can see from the pics above. Anyway, the tang patch was completely invisible when finished. I told the customer his gun had a large patch and asked him to call me when he found it. I haven't heard from him.
The termite holes in the above stock weren't just filled with epoxy, the areas were cut out and filled with wood. There must be four or five patches in total. If I would have tinted epoxy and filled the holes you would have seen them because the glue has a smooth texture when finished. The way I do it you have to carefully select your patches to the grain flows properly. With my method you have minuscule to no glue lines. Glue lines can be seen because they are smooth in texture.
Do this sort of thing any way you like. I always enjoy the "add some saw dust" advice. I think I'll continue to do it my way.