I think that would work actually. However, the main issue then would be people wanting to use their existing saves with an updated generated ISO with different ID. Perhaps I will add it as a third "save" option in the builder. And no rush on the save_banner.arc files, I will prolly be gone for the next 12 or so hours anyway. (logging off after this post)
That could pose an Issue, but to be honest, I doubt many will come back to this tool after they've made their ISO's once, unless they build a bad Newer version (Newer 1.01 and 1.02 had issues with world 3-6 and 3-7) And for those that do, I guess I'll throw together an icon for them. :/
My idea is that when the bat gets to the point where it asks what save slot, it'll have 3 options.
1. Share with NSMBW (No option to use custom save banners)
2. Universal Custom ID [KMNx] (No option to use custom save banner, same as 2 from previous versions)
3. Auto Full Custom ID (it'll apply the proper ID for the mod your building, and include Custom Save Banner patching based on your region and mod)