As explained, primary key and unique key names are not created/modified by Aurelius.
In the Data Modeler documentation there are several script examples for different tasks that you can use as a base for other tasks, and also learn from it.
Also, TMS Aurelius documentation explains the limitations and behavior of the update database when it comes to existing data and destructive commands. Some update operations are not performed indeed.
Here is a key snippet from it:
Since this method performs on a database that has existing object and data, it has some limitations. First, if you are unsure of the effects of schema update, it's strongly recommended that you check schema validation results before updating. Errors might occur when updating the schema, for example, if new schema requires a foreign key creating but existing data doesn't fit into this new constraint. See schema validation for a list of current valid operations and limitations.
Note that UpdateDatabase is a non-destructive method. This means that even if the validation reports that a data-holding object (table or column) needs to be dropped, the SQL statement for it will not be performed.