add Amplify.configure migration docs for config customizations

**Describe the content issue**:
A clear and concise description of what the content issue is. Is there content missing or is there incorrect content?

A customer reported the current migration docs don't have a section to migrate a manual Amplify configuration. The Amplify.configure method in v5 allows to override the default storage mechanism, set the AuthFlowType used by authentication flows, set a custom userpool endpoint, etc.

**URL page where content issue is**:
`amplify-js` repo Issue [#13740](https://github.com/aws-amplify/amplify-js/issues/13740#issuecomment-2301960254)