As far as I know, that is OK as long as the concrete of the base slab seals everything AIR-TIGHT.
Yes, in part this is probably even done deliberately, since the oxidation increases the surface area and is supposed to create a better bond with the steel. Once the concrete is applied, it is as you say, the oxidation process stops, because as the word already says, it requires oxygen, which no longer has access to the reinforcement through the concrete. I would be completely relaxed about this too.