Tanjamuse sent me their personal.ini. I'm posting the reply so everybody can benefit.
The include_subject_tags parameter under [epub] takes precedence over the one in [archiveofourown.org].
Unless you really do want different handling for different formats, move the include_subject_tags and other parameters to [defaults] instead.
Changing [archiveofourown.org] to [archiveofourown.org:epub] would also work.
Code:
## [defaults]
## titlepage_entries: category,genre, status
## [www.whofic.com]
## # overrides defaults.
## titlepage_entries: category,genre, status,dateUpdated,rating
## [epub]
## # overrides defaults & site section
## titlepage_entries: category,genre, status,datePublished,dateUpdated,dateCreated
## [www.whofic.com:epub]
## # overrides defaults, site section & format section
## titlepage_entries: category,genre, status,datePublished
## [overrides]
## # overrides all other sections
## titlepage_entries: category
## ...
[epub]
##...
include_subject_tags: extratags, genre, category, characters, ships,
## ...
[archiveofourown.org]
include_subject_tags: category