The bootstrap process uses the importer to load the initial set of data into the repository when it's started for the very first time.
Within /config/alfresco/bootstrap, you'll find the xml files that are imported. There's one called spaces.xml which creates the Company Home folder and its sub-folders i.e. data dictionary and guest.
So, you can adjust this file by adding the rule definition to the Company Home folder. What's the xml for the rule definition? The easiest way to generate is to go into the Web Client, create the rule on the Company Home folder and export the Company Home folder. The resulting xml will consist of the rule definition which you can copy into spaces.xml.
You can just change the existing spaces.xml, but if you upgrade, then you'll lose your changes. So, as with all customisations, you should use Alfresco's extension mechanism.
Within /config/alfresco, you'll find a bootstrap-context.xml file which lists all the processes (spring beans) that are executed during bootstrap. You can override any of one these beans by providing your own replacement definition of the bean. This is done by creating your own custom-context.xml (this can be any name) in /alfresco/extension. The bean you want to override is spacesBootstrap. You can copy its definition from bootstrap-context.xml. You'll want to replace the reference to alfresco/bootstrap/spaces.xml with your own version of spaces.xml which can also live /alfresco/extension.
To test, start Alfresco on a clean database/alf_data directory and the bootstrap process will be initiated.