Compare two databases and get the differences

Probably not

The view that may display native stored compiled indexes is CTX_INDEX_VALUES Or CTX_USER_INDEX_VALUES (depending on permissions and querying user). However, given that the index value length is only 500 characters, it is unlikely that it is stored there. (Just start selecting randomly from those indexes, if it exists, it will likely be there.)

Looking at the view design, however, it is unlikely that those virtual XML elements are stored, as it's much easier to compile them on the fly and then load them into memory.

Alternatively, CTX_DOC has a number of markup functions, but none indicate the ability to access native XML.

You may also want to explore the discussion around metalink: 122255.1 (Unfortunately, I don't currently have metalink access).

It may be easier to write your own parser-to-XML (as oracle has quite a few excellent native XML functions) than try to hack around the full text index.

Here is a brute force example that doesn't require modifications to the tables. It merely gives you information about what is different, it does not do anything to synchronize it.

Sample data:

--DROP TABLE tableA;
--DROP TABLE tableB;

CREATE TABLE tableA AS (
   SELECT level-1 ID, chr(level-1+70) bb, chr(level-1+100) cc FROM dual CONNECT BY level<=4
);

CREATE TABLE tableB AS (
   SELECT level ID, chr(level+70) data1, chr(level+100) cc FROM dual
   UNION ALL
   SELECT level+2 ID, chr(level+70) data1, chr(level+100) cc FROM dual CONNECT BY level<=3
);

SELECT * FROM tableA;
SELECT * FROM tableB;

Compare:

WITH UnionedRows AS
(
   SELECT * FROM tableA
   UNION
   SELECT * FROM tableB
)
SELECT ID, sum(MyCount),
   case
      when sum(MyCount) = 111 then 'In Table A and Table B - Identical.'
      when sum(MyCount) =  11 then 'In Table A.'
      when sum(MyCount) = 112 then 'In Table A and Table B - Different.'
      when sum(MyCount) = 101 then 'In Table B.'
      else 'Error.'
   end Status
FROM
(
   SELECT ID, count(*) MyCount FROM UnionedRows GROUP BY ID
   UNION ALL
   SELECT ID, 10 FROM tableA
   UNION ALL
   SELECT ID, 100 FROM tableB
) GROUP BY ID ORDER BY ID;

You will need to modify this code to use your primary keys, table names and database links, but the nice thing is that you don't need to list all the column names for every table.