refactor: wider dependency-injection and port cleanup for stores and services beyond the app boundary

## Follow-up from PR #11751

**Context:**
PR #11751 (https://github.com/Comfy-Org/ComfyUI_frontend/pull/11751) extracted the missing-model pipeline orchestration from `ComfyApp` and moved it to `src/platform/missingModel/missingModelPipeline.ts`, keeping `ComfyApp` as a thin caller/adapter. However, full dependency-injection and port cleanup for stores and services beyond the immediate app boundary was intentionally deferred.

**Task:**
Continue the dependency-injection/port cleanup for stores and services that remain tightly coupled beyond the app boundary, further decoupling platform modules from app-specific concerns.

**Relevant files:**
- `src/platform/missingModel/missingModelPipeline.ts`
- `src/scripts/app.ts`

**Requested by:** @jaeone94 in https://github.com/Comfy-Org/ComfyUI_frontend/pull/11751

┆Issue is synchronized with this [Notion page](https://app.notion.com/p/Issue-11754-refactor-wider-dependency-injection-and-port-cleanup-for-stores-and-services-beyond--3516d73d365081ca8ed7dc5e66a94244) by [Unito](https://www.unito.io)