One solution I can imagine, although not currently available AFAIK, would be to have two different auto-adding folders, one for the mangas and another for the "classic" ones.
One would read metadata from content, the other from filenames.
Action Chains plugin might make this possible, if there existed an action to toggle that Calibre behaviour option.
see:
https://www.mobileread.com/forums/sh...8&postcount=14