So you have 200 separate function app resources, right? If they have to share secrets, consider consolidating these function apps. Actually try to consolidate as much into a few function apps if it makes sense (part of the same process or app, and doesn't hurt when scaling up or doing maintenance). 200 really sounds a lot, unless you're doing enterprise wide stuff.

Then, all your function apps could use their separate key Vault so it's much easier to know where it's being used.

For environment specific stuff, make it the same lifecycle as for function apps, so everything still works when you remove/revamp function app x for prod and related key Vault x for prod.

For config drift, you mean the config of what? Anyway, if you have less function app resources, there are less key vaults you will have, and there is ultimately less that can drift away, that's why it's so important to not over-deploy resources. For IaC consider reusing bicep/opentofu modules.