Nah, it'd be fine Bob, anodizing can be measured in microns, so not enough to affect the seal of mating surfaces.
Contact Andy Morris, AKA 736cc on this site Fuzzy, he runs a Honda 750 restoration business, and has developed a case coating system, that looks like the cases have been highly polished, and I think he does a "changeover" deal?
He sent me some pics of a complete coated CB750 engine awhile ago, and from memory, they looked really good! Cheers, Terry.