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I never use the SQL parameters in FME to create the Spatial index on an Oracle table.
To control what you need to do I would create the Metadata before and the Spatial index after inserting the data into the table using SQL scripts or statements in a SQL application (SQLDeveloper,SQL*Plus or Toad).If you need to reload a big table,dropping the Spatial index before inserting and recreating it after inserting the data will boost your performance.
Creating the Metadata before inserting will allow you to add a SRID to the geometry as FME reads the Metadata to define the SRID.
Are you able to make use of the Advanced Parameter that can run after the translation,found on the writer?Instead of using the dedicated indexing parameters...
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