I have not seen the film "The Crown Prince". However, the incident with the Jewish girl is apparently true, as it is mentioned in Brigitte Hamann's biography "Kronprinz Rudolf" on page 151. It took place in Prague when Rudolf was stationed there in approx 1878 and Rudolf was so upset and depressed when the girl died that he had to be treated by the "Nervenarzt" Dr. Moritz Benedikt, whose daughter later wrote about the incident.
The funeral ritual is also true....before the remains of any of the Habsburgs were admitted to the crypt the monks asked "who wishes to be admitted?". On hearing the answer "The Emperor of Austria" they would respond "We know him not". It was only when the answer was " XX (i.e. the first name of the deceased), a poor sinner" that the door was opened and the coffin could be brought into the crypt. However, it is said that the ritual had fallen into disuse in the 19th. century and was only revived for the funeral of Empress Zita.
Cheers,
GREENOWL