I think you have made the right decision, yes, some scratches and marks can be improved greatly on box calf, but some scratches that are deep, although they might be blended in somewhat, cannot be removed and are permanent. There are quite a few stories here about bags that have gone in for spa at Hermes with deeper scratches and the owners have been disappointed that they haven't been able to remove them. Best to spend out on a bag which is right to begin with, there are lots of black box Kellys out there in fantastic condition, even vintage bags, don't settle and hope the bag can be brought up to scratch, sometimes they can't. My best advice is any bag you buy, make sure you are happy with all aspects of it before you pull the trigger. I would hate to see you buy a bag and then you are unhappy because those marks won't come out.
Keep looking, the right bag will appear soon!