Python CI

unify flags (#328) #1381

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Run time

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Job	Run time
Lint & Type Check	1m 47s
MCP End-to-End Tests	48s
Batch Evaluation Tests	1m 10s
Core Tests (Python 3.12)	7m 21s
Core Tests (Python 3.11)	7m 2s
Core Tests (Python 3.10)	7m 7s
Upload Coverage	6s
	25m 21s