Amplify codegen doesn't support namespace queries/mutations

### How did you install the Amplify CLI?

npm

### If applicable, what version of Node.js are you using?

v20.10.0

### Amplify CLI Version

12.8.2

### What operating system are you using?

Mac (also with devcontainers Debian 11 bullseye)

### Did you make any manual changes to the cloud resources managed by Amplify? Please describe the changes made.

N/A

### Describe the bug

Hi, my schema has namespaced queries/mutations and when running `amplify codegen` it's failing when trying to generate types. The following repo https://github.com/sescotti/amplify-namespaced-gql reproduces the issue.

I'm getting the following error:

```bash
node ➜ /workspaces/namespaced-graphql (master) $ amplify codegen
✔ Generated GraphQL operations successfully and saved at src/graphql
⠋ Generating.../GraphQL request: Field "create" argument "input" of type "CreateCustomerInput!" is required, but it was not provided.
.../GraphQL request: Field "create" argument "input" of type "CreateOrderInput!" is required, but it was not provided.
.../GraphQL request: There can be only one operation named "Customer".
.../GraphQL request: There can be only one operation named "Customer".
.../GraphQL request: Field "get" argument "id" of type "ID!" is required, but it was not provided.
.../GraphQL request: There can be only one operation named "Order".
.../GraphQL request: There can be only one operation named "Order".
.../GraphQL request: Field "get" argument "id" of type "ID!" is required, but it was not provided.
✖ Validation of GraphQL query document failed
```

### Expected behavior

GQL types correctly generated

### Reproduction steps

1. (Optional) Open repo in devcontainer
2. Run `amplify codegen`

### Project Identifier

Learn more at https://docs.amplify.aws/cli/reference/diagnose/
⠋ Creating Zip
No Amplify backend project files detected within this folder.
✖ Creating Zip

### Log output

```
# Put your logs below this line

```

### Additional information

Same thing happens when collecting the schema from an existing AppSync API when using the `--apiId` arg

### Before submitting, please confirm:

- [X] I have done my best to include a minimal, self-contained set of instructions for consistently reproducing the issue.
- [X] I have removed any sensitive information from my code snippets and submission.