Right now, when a value that is an instance of java.util.Collection is passed as parameter value, it will be added as parameter list as can be seen here: https://github.com/hibernate/hibernate-orm/blob/master/hibernate-entitymanager/src/main/java/org/hibernate/jpa/internal/QueryImpl.java#L237
When having a custom user type that implements java.util.Collection this will obviously not work as expected. The parameter will be expanded and binding the values will not use the custom user type.
Since the parameter metadata is already known, it shouldn't be that hard to check if a parameter should be bound as collection or as a single parameter.