The FILE_GDB writer has this capability, it saves a postprocessing step in ArcGIS
Released
Support field indexing in GEODATABASE_FILE writer
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+22- Enthusiast
Also GEODATABASE_SDE where the SDE table does not exist or does not already have field indexes.
+21- Safer
https://docs.safe.com/fme/html/FME-Form-Documentation/FME-ReadersWriters/geodatabase/GEODATABASE_FILE_writer.htm
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