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Trigger ART tests: Use ConfigFlags instead of TriggerFlags for triggerMenuSetup

Rafal Bielski requested to merge rbielski/athena:trig-test-ConfigFlags-preExec into master

After the move to the new flags in Trigger congfiguration in !35402 (merged), !35481 (merged), the reconstruction preExec has to be adapted. This is done here for three tests using this option. In addition the flag is also set in the PEBDS test options.

Fixes ATR-21843

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