[Bug]: Preserve autoentity-generated entities in multi-source MCP runtime configuration

### What happened?

When multiple child configurations use SQL `autoentities` with MCP enabled, DAB discovers entities during child/provider initialization but `describe_entities` returns `NoEntitiesConfigured` from the final merged runtime configuration. A parent with one child and each child tested independently work, while a parent with two or more children reproduces the failure.

Expected behavior: all generated entities from every child configuration should be present in the shared runtime configuration and returned by `describe_entities`, with each entity mapped to its originating data source.

Observed behavior: startup completes successfully and `dab validate` reports discovered entities, but MCP sees no usable entities. The issue appears to occur while propagating generated autoentities from per-child/per-datasource metadata providers into the shared root `RuntimeConfig.Entities` collection used by MCP.

This is a child investigation item for https://github.com/Azure/data-api-builder/issues/3711. Please verify the runtime merge sequence, generated entity collection, and entity-to-data-source mappings across two or more child configurations.

### Version

2.0.9

### What database are you using?

Azure SQL

### What hosting model are you using?

Local (including CLI)

### Which API approach are you accessing DAB through?

MCP

### Relevant log output

```Text
Startup completes with `Successfully completed runtime initialization`, but `tools/call` for `describe_entities` returns `NoEntitiesConfigured` after using a parent config with two or more child configs containing `autoentities`.
```

### Code of Conduct

- [x] I agree to follow this project's Code of Conduct