refactor: general workflow serialization and type-boundary cleanup outside the missing-model refresh path

## Follow-up from PR #11751

**Context:**
PR #11751 (https://github.com/Comfy-Org/ComfyUI_frontend/pull/11751) removed the unsafe `graph.serialize() as unknown as ComfyWorkflowJSON` cast in the missing-model refresh path by introducing `FlattenableWorkflowGraph`/`FlattenableWorkflowNode` contracts. However, broader workflow serialization and type-boundary cleanup outside the missing-model refresh path was deferred (also partially tracked in #11679).

**Task:**
Audit and clean up remaining places in the codebase where `LGraph.serialize()` output is unsafely cast to `ComfyWorkflowJSON` or similarly mismatched types. Extend or reuse the flattenable workflow contract where appropriate to eliminate unsafe type assertions.

**Relevant files:**
- `src/platform/workflow/core/utils/workflowFlattening.ts`
- `src/platform/workflow/validation/schemas/workflowSchema.ts`
- `src/scripts/app.ts`

**Related:** #11679

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

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