It took until I came across a vanilla fish before I got the fishy business advancement.

Also the advancement "Tactical Fishing"

There is no way to add support without overwriting the vanilla advancements. If I can make the advancement overwriting configurable I'll implement it, otherwise there is not much I can do.

Yea no way to make it configurable.
You can use this for "fixing" the Fishy Business advancement with a resourcepack:
https://gist.github.com/GirafiStudios/e3871bced3c48de1ab550958d5a6b625

So the advancement json files overwrite the vanilla ones instead of just adding more conditions? So if two mods were to mess with the same advancement one would be overwritten?

Exactly, which is why I don't want to add it directly to Aquaculture 2.