Well, it's not perfect, but here's what I've figured out for Confluence so far, and I think it should be applicable to other skins.
I added new source flags by editing XBMC/addons/skin.confluence/720p/IncludesCodecFlagging.xml
XBMC in this case is the parent folder to the
userdata folder (wiki).
There's a section called "<variable name="typehackflagging">"
It has values that look like this: "<value condition="substring(ListItem.FilenameAndPath,vhs)">vhs</value>"
The first "vhs" is what name in the file path (be it the file name or any part of the folder/server path) needs to match for that flag. The second "vhs" is the name of the image tag that XBMC puts for that flag, which it loads from
XBMC/addons/skin.confluence/media/flagging/video/
So I made a test where I added this "<value condition="substring(ListItem.FilenameAndPath,anime)">anime</value>"
and I made a small 100x48 PNG image that said "Anime" in it and saved it as anime.png to XBMC/addons/skin.confluence/media/flagging/video/anime.png
(in Confluence's case this folder was empty and didn't have any images. This is because all of the images are loaded into a texture packer file for faster loading. However, placing new individual images in this location still works.)
Sure enough, it shows this flag when you select the entry, depending on your list view.
The next step would be having a skin view that shows flags in the list and not just when a specific entry is selected. I haven't gotten that far yet, but hopefully this is a start in the right direction.