chore(config): resume config handling

[binaryaaron]

• fix: upgrade xgrammar and use new structured gen method
• chore: address cr
• chore: last bits
• fix: update config overrides for generate only runs

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[codecov]

Codecov Report

❌ Patch coverage is 82.71605% with 56 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
...s/benchmarks/test_generation_structured_methods.py	49.09%	56 Missing ⚠️

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[binaryaaron]

closing in favor of #549