If you imagine a pit as a pothole.. if it is deep you want to get the edges of the hole tapering into it so that when its blued it will be less apparent... the only way to completely (and pedantically!) Get rid of all pitting is to bring all the surrounding material diwn to the same depth as the deepest pit! As said earlier in this thread, trying to smooth out the pits locally should be enough for a satisfactory finish. Bluing will not hide any pits, but as long as they dont have defined edges it should look good enough.
Personally ive never went the whole hog and really tried for a perfect finish.. I just dont have the tools to make it simple.. like you I have spent hours and hours with wet n dry getting it as good as I can then cold bluing...ive never had a gun hot blued or rust blued so I really have no knowledge of how these finishes deal with faint pitting. I imagine its pretty much the same.
As long as I get a nice even blue I dont mind tiny blemishes where pitting used to be.. after all its an old gun.. as long as its protected from further rusting im happy... its like picking up a mangy mutt from the pound!