If you think a tag is misapplied - instead of starting a thread bitching about it, use the REPORT button at the bottom of the OP. It something isn't in the game - it isn't supposed to be tagged.
As for your example, many games have certain tags here that have the ability to have that content with either optional relationship variables in-game or through fan-made mods because the creators would lose their patreon access if the content was included in the base game. And without their patreon access, their games may not be made or continue to be made. So some leeway should be considered.
See #2 here. Also make sure the definitions for the site match what you think the tag means.
Obviously, a lot of the "totally not incest" games on here were fully intended to be incest games. But it gets removed to skirt Patreon rules and such. If it's fully what the author intended, then I think having the tag is fine, even if a mod is needed. If someone is just modding your legit childhood friend into your sister then no, there shouldn't be a tag.
If the mod is also shared in the same thread I don't see why not, tags are used for the thread as a whole and not just the base game.
For instance if the base game is shared together with extra dlc featuring unique content, then all the dlc content should also be tagged in the thread.
Now if the mod/dlc was not available in the thread for some particular reason then I would agree with you.