In my past life as a QC manager, the galvanizer we used addressed areas where the HDG was rough or had runs and drips(icicles). I think they used a scotchbrite pad or something similar that removed the roughness without cutting into any base material. Maybe that would be a solution for you on the flanges' mating surfaces.
Not sure whether they are any ASTMs or specific code references that address your issue about the sealing surfaces...maybe someone else can answer that for you.