Just a quick clarification: "chan" in Japanese is an honorific, similar to "san" (the equivalent of "Mr." or "Ms."), but much more casual and less formal than "san". It's often used when addressing a child, which I guess is where the fandom term came from, but it can also be used as a sign of affection between adults who are close to each other.
As for the main discussion, I've been pondering the issue myself, without any easy answers. Someone once raised the question of Rukia in the manga/anime Bleach: she appears to be a teenager, but in human years, she's something like 70 years old. However, her race, the Soul Reapers, appear to age very slowly, so it's possible that she really is a teenager by their standards, and on top of that, she attends high school with the main character as part of her disguise when she's in the human world.
And I was once involved in a fandom where an author was accused of pedophilia because she wrote an explicit fic involving a character's chibi form. (Sort of a minaturized, childishly cute caricature done for humorous purposes in manga and anime.) The character was not underage--in fact, the character wasn't even human, but was actually an angel--but because it looked like a child, people were offended.
I would say if a character looks and/or behaves like a child/teenager, it's probably best to label the story "chan" or "underage" to be on the safe side, and people can decide for themselves if they want to read it. (Or view it, in the case of fan art.) Especially for a multi-fandom archive, where people might not necessarily be aware of the technicalities about the characters' ages. And the author could clarify the issue in the author's notes if they wish.
As to what the age line should be for chan, I have no idea. Personally, I started warning for any sexual situations involving characters below the age of 18, just to keep it simple. Although to be honest, I rarely write underage stories, since I write mainly Snupin in the Harry Potter universe, and Leon/D in the Petshop of Horrors fandom.