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Operators and adapters which call Operator.getRuntimeInputSchema() always expand capture fields, therefore these may cause runtime errors when using the default FLATTEN strategy. Few operators have a "CaptureStrategy" property which can be set to NEST instead. If all operators and adapters making this API call had this property, then one could make a global operator-parameter settings which changed the default to NEST for a project.
Currently if one uses operators or adapters that call getRuntimeInputSchema() (there's no way to know in advance with built-in elements) and the expanded field names collide with top-level tuple fields, the only workaround is to add additional boilerplate processing upstream to all impacted modules to avoid the collision, and potentially more operators downstream to undo the transformation.