Hi,
At the moment, you can have only one per environment.
Though it could possibly support several projects but we didn't tested it.
Here is what I would do
1. Create a new unmanaged solution, add all components included in the base kit
2. Update the "Documentation Automation Application" to allow multiple configuration. Put "true" on visible field

3. Create a new Configuration in the Document Automation Application for each project
Alternatively, you could duplicate the "Document Automation Application" for each projet, create a "Project Name" column in the "Document Automation Configuration" table and in the Configuration page change the query to filtering on this particular "Project Name" value.
You would probably have to do similar filter in other parts of the application to only get the documents processed for this project
4. Duplicate the the flow "Document Automation Email Importer" for each project.
5. In this flow, update below action adding a filter to the proper configuration (E. g. aib_documentautomationconfigurationid eq %GUIDVALUE%)

This may work but again was never tested.