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You don't need to change the "%" to a "_" in this instance as the cls method is being passed a string literal. This works fine:
print(iris.cls('%SYSTEM.OBJ').Version())
InterSystems IRIS Version 2022.1.0.209
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You can also set this at a workspace or user level by going into Settings -> Extensions -> InterSystems ObjectScript and updating the "ObjectScript Compile Flags" setting: