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...

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.