I have a problem with shared headcanon
Shared headcanons are distinct from fanon.
Fanon is where a fan theory/headcanon has come to be accepted as canon by the fan community despite not being supported by canon--in fact, often being refuted by canon. As a fan creator, it's usually best to avoid fanon whenever possible.
Shared headcanon is a different animal. A shared headcanon occurs when one fan creator does something, it's popular, and then it starts getting copied by others. Fanon usually starts as shared headcanon, but not all shared headcanons eventually become fanon.
A major type of shared headcanon is the preferred ship. From one fandom I spend some time in, Yuri on Ice, there are tons of these preferred ships. For example: Guang-Hong and Leo are always shipped together. It's rare to find either of them prominent in a story where the ship does not occur. At least it makes a modicum of sense, as they spend a lot of time together and are shown to be good friends. Michele/Emil on the other hand is less so, as Michele constantly displays irritation towards Emil. Perhaps least explicable is the preferred ship of Phichit/Seung-Gil, as those two never interact directly. Their only interaction being a brief dream sequence of Phichit's in which several skaters, one of them Seung-Gil, appears.
Now there's nothing wrong with these ships as such. What I have a problem with are these ships becoming the default. When you like a side character, but the only content you find for them is a ship you don't like, that's a frustrating situation.
Another type of shared headcanon is the character headcanon. To look at My Hero Academia fandom as an example: the character of Sero Hanta is very often depicted in fanworks as a cannabis smoker, and of Hispanic ancestry (not always both, but often yes--and yes, unfortunate implications). And if you are looking for a different characterization of Sero, good luck.
Can something be done about it? "Exclude" tags in AO3 are great, but that only hides the pieces you don't like. The dearth of side character without the headcanons you dislike remains.
When it gets down to it, you might have no other choice but to write the story you want to read.