This is common on the 400's that i have done over the years.
The gold colour is i think Aludine coating. not sure why Honda did this, Aludine coatings can be done on aluminium surfaces to give extra protection or as a base/primer prior to painting.
I doubt you have mismatched cases, but easy to check if the engine is apart. bolt the cases together and mic the bores. but if it's been running for years then i don't think you have anything to worry about.
Kevin