There isn't a lot of config and some things are not compatible with other mods and some could benefit from other mods.

We could begin with crates by a kind-of in-depth config on each crate and what they can drop, the chances of each item, and what can come out of the crates.

Go Fish is already fully configurable through data-packs. You can see all the loot tables used by Go Fish here. Go Fish also overrides the standard fishing loot table here. As an example, the Diamond Crate table is found here. If you want to modify these or provide compatibility between multiple fishing mods, you can ship a data-pack that overrides one or more of these loot tables with your modpack/server.

*note: Go Fish also injects into the standard/overworld fishing loot table here, because loot tables do not have an append option/functionality, and I would rather not nuke fish from other mods. I could add a config option for these in the future, but there really isn't anything you would need to config here, outside completely removing a fish from the drop tables.

tl;dr: data-packs already give you full control over drop rates, what crates can drop, item chances, etc.