As mentioned in the document https://docs.aws.amazon.com/apigateway/latest/developerguide/api-gateway-caching.html, "When a cached method or integration has parameters, which can take the form of custom headers, URL paths, or query strings, you can use some or all of the parameters to form cache keys. API Gateway can cache the method's responses, depending on the parameter values used." So where you define the cache key will determine at what point will the incoming request be evaluated against the cached keys.
If you have defined a proxy resource only and no other resource in the API, then the settings on the proxy resource will apply on all resources. If there are more specific resources defined, then the settings on those specific resources will apply to those specific resources and the proxy settings will apply to every other resource. To understand how proxy resources work, please take a look at https://docs.aws.amazon.com/apigateway/latest/developerguide/api-gateway-method-settings-method-request.html under this section "Use a proxy resource to streamline API setup".
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