applegaa, the word 'tags' is ambiguous, and metadata entries are not the same thing as what ends up in Calibre's Tags column, aka 'subject tags'. So I'm not 100% sure I know what you are saying. But I will make an attempt.
I think this does it:
Code:
[www.scribblehub.com]
# Remove genre & extratags from Calibre Tags.
include_subject_tags: category, characters, ships, status
# Add a custom column setting to the list for genre,
# flag 'r' for replace to overwrite more generic setting
add_to_custom_columns_settings:
genre=>#yourcategorycol,r
If that doesn't help, please provide a concrete example with story URL (SFW please) and exactly which values you want and don't want where.