refactor(module-graph): clear the three Sonar issues #743 left #746

#743 merged with new_violations = 3; I checked the quality gate status but not the count, which is the rule:

• S3776, cognitive complexity of build_module_graph (16 > 15);
• S3776, cognitive complexity of transitive_reduction (18 > 15);
• mixed assertion argument order in tests/unit/test_module_graph.py.

Done when: Sonar reports 0 new issues on the follow-up PR, with behaviour unchanged (same tests).

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