Projects are not a good fit for using directly in the Bluemix environment.
The blog posts you have read (Creating a Node-RED deployment pipeline to IBM Cloud · knolleary) explains why.
The boilerplate is optimised for ease of use and getting started. Applications running in the Cloud Foundry part of IBM Cloud cannot treat their local file system as persistent storage - any time the application is restarted the file system is wiped back to its original state. This is why the Node-RED boilerplate comes with an instance of the Cloudant database service; giving it somewhere to store its flows.
The projects feature relies on the local file system being persistent so it can maintain a git repository there. When running in a Cloud Foundry environment, that file system will be reset whenever the application is restarted.
