The black stuff is Ferrous Oxide. It is stable and inactive. The red rust was Ferric oxide, which is the active form of iron oxidation. The remover passivated some of the original rust and turned it into its stable cousin. The ferrous oxide is hard, but also brittle. If it is thick enough that it would crack if the metal flexes, or high enough that it would cause problems with the wood moving over it, you want to remove it so it will not allow more oxygen and moisture into the cracks to start more rust. If the metal is solid, it should do well with a good coat sealer or wax.
If you do sand it or grind down high spots, etc, you may want to hit it again with the rust remover, because you may be exposing active Ferric oxide encapsulated in the black ferrous oxide. The only way to remove the etching and pits is to polish them out.
To remove it, a rubberized abrasive wheel is best, with a smooth stone (think dremel grinder if the areas are small) second. Use a light touch. It can be removed with a disk sander, but it is difficult, because the Ferric oxide is harder than the bare cast iron next to it. Wet/Dry paper will work, but try to get the pressure directly on the heavier spots to start with, and finish it up with a sanding block backer to avoid shining up the surrounding metal and leaving a hump of the black stuff.
Go
) for it you can go this route:
