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Fix flags in BPHY25.py

Thomas Strebler requested to merge tstreble-main-patch-24995 into main

Follow up to !69731 (merged)

SlimmingHelper should use flags and not ConfigFlags as input argument https://gitlab.cern.ch/atlas/athena/-/blob/main/PhysicsAnalysis/DerivationFramework/DerivationFrameworkCore/python/SlimmingHelper.py?ref_type=heads#L79

Updated to use flags everywhere in the config for consistency with other CA configs

FYI @xchen

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