[ktz03]

Fixes #938, reported by @HenryZhou19.

With two dictionary config scopes, a newly supplied config update loses its added flag because the second scope fills its presets before determining which fixed keys were added. This also bypasses the unused-update check: a misspelled parameter that raises ConfigAddedError with one dictionary scope is silently accepted with two.

Move preset filling after the addition/modification summary is collected, matching the ordering already used by ConfigScope. Add regression tests for the public ConfigDict preset path and for Experiment.run with one, two, and three dictionary scopes, covering both consumed and unused new parameters.

Validation on Windows, Python 3.11.16, NumPy 2.4.6, and pytest 7.1.2:

• The seven new cases produce 5 failures and 2 passes on the unchanged base; they all pass with the fix.
• Config and experiment tests: 311 passed.
• Full python -m pytest tests/ -q -rs with pandas 2.3.3: 726 passed, 12 existing skips.
• pre-commit run --all-files: Black and Flake8 passed.

The current source requires pkg_resources, so the environment uses setuptools 80.10.2. With pandas 3.0.6, the full suite has the same unrelated TinyDB dataframe-serialization failure on both base and fixed trees; pandas 2.3.3 was used for the passing full run. No dependencies, skips, or CI settings are changed by this PR. Other Python/platform combinations and live observer services were not tested.