Hmm. I've seen others say this just now, but I think when you're interacting with work where fanon is so strong, it's gonna be important to keep in mind and be aware of what's really canon in the given material and what is a headcanon + what's part of non-canon supplementary material, and may have been used as inspiration. (Inspiration also doesn't mean something was adapted 1-to-1, but that it was taken as an idea, and necessarily isn't the same/functions the same as in the inspiration source either.)
Zelda has...a lot of this stuff, so it'd be very easy to get confused, especially as some headcanons are so common that to many peoples hearts they're basically canonical already (I do that too). The only truly Canon thing are the games, though, and that's what LU mainly revolves around (Although Jojo is hiding two mystery Links from us still, and one of them looks an awful lot like....)
The Manga aren't canon to any of the games, but used as a place of inspiration for many anyway, especially FSA fans being basically exclusively manga fans. Plus some games have multiple manga adaptations as well, especially the older ones not done by Himekawa. Not to mention the Non-canon cartoon and all...Hell, the entirety of Hyrule Warriors isn't canon to the Zelda Timeline, but Warriors as a character is in Linked Universe (while the games events aren't.) It's a bit to keep track of.
I guess the strongest example of this in the comic itself is FSA+, a beloved manga which many Four, Shadow and Colors fans use as a basis...but one that isn't directly canon to LU. We don't even know how Jojo will handle Shadow yet, if she will at all, if he will be how he was in the manga...all we know is that she took which colors portrayed what aspects of Fours personality as inspiration, which is similar but also not the same as the manga.
Only saying this because I think this is important to keep in mind while being in a fandom. So that when you read someone elses work, their art, see a different take than usual, or even interact with Jojos own choices in the comic, you don't feel disappointed, upset or confused by a headcanon you thought was canon, so that you know what someone headcannoned and what is canon. (Ex: "Wait, didn't Twilight canonly get his arm cut off?" <- This only happened in the manga, never ingame. Adapt it if you like of course, but don't confuse it!)
If anything, I think everyone should be encouraged to take what they like and decide for themselves what feels right for them to write and stuff. Do what makes you happy, but respect others headcanons and their choices too. Its always fun to discuss them, right? Sometimes you may see someone elses headcanon and go "Wait, I like that!". In the same vein, if you see a headcanon and decide it's not your cup of tea, don't feel pressured about it either. Make your own choice on what you like and choose to implement and adapt into your own interpretations. Fanwork and exploration should be encouraged, and most importantly enjoyed, and characters can be played with like touys and bended into all shapes and sizes. Yay
