Obviously this won't work for every scenario, but I think it's a better starting point that using "age of consent" since that's obviously going to vary and in some situations, not even be applicable. And of course, you can't use the same standards for characters who aren't human and couldn't possibly be mistaken for human. In that case they would have to be adjusted for whichever standards of maturity and so on are applicable for that particular universe.
In the situations you mentioned, I'd put most of those under the catagory of "questionable consent". As for the characters you mentioned... I would hope that somewhere in the fic summary there would be like "this is a sexually explicit fanfic involving Character X", and I would hope that'd be sufficient warning for anyone.
I think you're absolutely right about the last point; "sexualized innocence" is a large part of what chan is, and while it's not easy to find an objective standard for something like that, it is a good "rule of thumb" that authors should keep in mind when they're categorizing fiction. In fact I think a more feasible thing to do, rather than having rules like "if your character is younger than this, then it's chan", would be something like "Does your story contain situations like X, Y, and Z?" and if so, then the author should consider the appropriate warning label. Obviously this system wouldn't be perfect, but neither would a system of strict rules, and this would at least give the author more freedom to consider the standards that exist in the universe they're writing about.