fix: reconcile dependency matrix baseline

[Pigbibi]

Summary

• reconcile six stale dependency-matrix refs with live consumer pins
• replace the shared canonical QPK-pin test assumption with explicit per-consumer baseline pins

Validation

• Python 3.12 focused RED before matrix repair, then PASS
• Python 3.12 full unit suite: 120 passed
• generated matrix semantic delta: exactly six refs
• strict checker: 30 files, no missing files or issues
• config/runtime/package build, Node 22 JS checks, actionlint 1.7.12, and diff gates passed

Scope

• only internal_dependency_matrix.json
• only python/tests/test_internal_dependency_matrix.py