It does, very significantly.
Under the primary designated offences, the court is not required to make the order if it is satisfied that the person has established that the impact of such an order on their privacy and security of the person would be grossly disproportionate to the public interests and the protection of society and the proper administration of justice, whereas if you are in the secondaries, it says:
In deciding whether to make the order...the court shall consider the person’s criminal record, whether they were previously found not criminally responsible on account of mental disorder for a designated offence, the nature of the offence, the circumstances surrounding its commission and the impact such an order would have on the person’s privacy and security of the person
There is much more to be considered, but the really significant difference is that the crown must apply for the secondary, whereas a judge shall make the order for primary “unless...”.