docs(py): update PARITY_AUDIT.md with PR status, middleware taxonomy, and merge order

Comprehensive update reflecting current state of all merged and open PRs:

Merged PRs reflected:
- #4511 (G5+G6: span_id + X-Genkit-Span-Id) → marked Done
- #4507+#4508 (G11: CHANGELOG.md) → marked Done
- #4509 (plugin test coverage uplift) → marked Done
- #4505 (PARITY_AUDIT.md baseline) → marked Done
- #4488 (sample naming, py.typed, check_consistency) → marked Done

Open PRs tracked:
- #4516 (G1+G2: model middleware storage)
- #4514 (Transfer-Encoding fix)
- #4513 (G18: multipart tools)
- #4512 (G20-G22: constructor parity)
- #4510 (G3+G12-G16: middleware functions)
- #4504 (Checks plugin)
- #4495, #4494, #4401 (bug fixes + reflection v2)

New content:
- Middleware Taxonomy section with 4-layer diagram
- Decision guide for which middleware layer to use
- G38 gap (auto-wiring via get_model_middleware)
- PR merge order graph with file conflict matrix
- Updated summary metrics and phase tables

Author: yesudeep