It'd be nice to have a config file that let us disable structures - perhaps even mass-disabling any structure with certain features? (e.g. disabling worldgen for anything that has an Enchanting Table in it).

For people looking at this:
You can already disable structures from Formations Overworld with a datapack the same way you would for vanilla structures. The default structure sets from Formations Overworld can be found here https://github.com/SuperMartijn642/FormationsOverworld/tree/master/src/generated/resources/data/formationsoverworld/worldgen/structure_set. Simply overwrite the the sets with a datapack and exclude any structures that you don't want to spawn.

As for adding a config:
I may still add a config (or something similar) to disable structures as the vanilla way is not the easiest or most intuitive, but I am not sure when or in what form if it all.

yup that would be great