Dear Vlad,
I tried to use the second variation you provided, but it did not worked.
At first I used GenerationType.AUTO with hibernate.hbm2ddl.auto=update, but then the init script is not executed.
When I a changed it to hibernate.hbm2ddl.auto=create, then it read up the file, but again the indices collided.
What can the solution be to both use my import script and have Hibernate properly inject id values well.