BTW org.hibernate.dialect.pagination.SQLServer2005LimitHandler.getProcessedSql(), as its javadoc says, produces queries like

 WITH query AS (
   SELECT inner_query.*
        , ROW_NUMBER() OVER (ORDER BY CURRENT_TIMESTAMP) as __hibernate_row_nr__
     FROM ( original_query_with_top_if_order_by_present_and_all_aliased_columns ) inner_query
 )

According to SQL Server's docs for ROW_NUMBER

There is no guarantee that the rows returned by a query using ROW_NUMBER() will be ordered exactly the same with each execution unless the following conditions are true.
[...]
Values of the ORDER BY columns are unique.
[...]

However, ROW_NUMBER() OVER (ORDER BY CURRENT_TIMESTAMP) does not satisfy this condition. If i misunderstood the SQL Server docs and this is correct usage or ROW_NUMBER(), then CURRENT_TIMESTAMP could be replaced with constant expression (e.g. 1) – not to give an impression that there is anything sorted there.
On the other hand, if I understood right the docs, the correct usage of ROW_NUMBER() would be to move the original order by clause into ROW_NUMBER() OVER (ORDER BY ...).

If such a change was applied, then as I side effect, the "SQLServerException: A column has been specified more than once" error would not appear, as SQL Server is more permissive when it comes to ROW_NUMBER() OVER (ORDER BY ...) contents.