This is a fantastic idea and one that is mentioned here (please add your comments):

https://knowledge.safe.com/idea/18790/workbench-connects-directly-to-revision-control.html

With the current FME Server Version Control functionality, our team shared that: pushing files from GitHub to FME Server (ie *pulling* from a remote Git) is not possible as of right now for a couple of reasons:

1. We cannot bypass the Publishing Wizard which is responsible for dictating how FME Server will run the workspace (updating the database, registering services, allocated resources etc). In fact, a user can't just drop a workspace into the repository home folder which is what pulling does. FME Server will see that the workspace doesn't exist because the database does not contain that workspace.
2. Pulling leaves the risk of merge conflicts which would require manually editing of the .fmw files which is obviously very difficult. More info here: https://www.git-tower.com/learn/git/ebook/en/command-line/advanced-topics/merge-conflicts