site is used to determine GC settings both in INI and from GUI.
Honestly, I never really considered anyone changing
site--and I would recommend against it.
Instead, I suggest you modify
publisher. For historical reasons, FFF uses
site internally while
publisher is copied from
site and used to populate Calibre's Publisher column and (by default) on title page.
Doing so would require you to use the original
www.fanfiction.net, etc in
generate_cover_settings
I've tested it and
replace_metadata on
site applies to GC settings as I expected.