If the pits are small they won't really get filled in, but the rough texture of the parkerizing will help hide them. If its a part that is going to show I'd remove them if I was concerned about them showing. Of course since you have the ability to parkerize now why not park it and see how it looks. If the pits show too much you can sand them out and parkerize it again. If you're going to cover the parts in gunkote and the pits are big, you can fill them in with jb weld and no one will be the wiser if you do a good job.