Yes, As a best practice, initially during the development phase, you should store the policies in ui.content, making sure that the /conf folder is mode="merge". This will setup and help future developers build a base project on their local machines. Ideally during the development of your editable templates, your ui.content.../conf should be closely identical.
Since in your AEMaaCS service has access to the crx/de, on every code deployment I would delete the /conf/my-app/...templates and policies, as developers are continuously working on this.
Now moving into Staging, you cannot push any new changes to /conf anymore (after the first push), and would need manage the policies via the AEM template editor UI.
Now moving to production, preferred, you'd need to content package the /conf/my-app, into the production environment.