The reason why we chose it at the time was because of the reason you mentioned. git-annex was really difficult to set up and manage in a team environment and the fact that it used a separate branch made things difficult for those new to git (we were constantly hunting down lost files on peoples drives).
The other major plus for us was that the files weren't symlinks. This made our deployment process easier since there was one less edge case to check.
The reason why we chose it at the time was because of the reason you mentioned. git-annex was really difficult to set up and manage in a team environment and the fact that it used a separate branch made things difficult for those new to git (we were constantly hunting down lost files on peoples drives).
The other major plus for us was that the files weren't symlinks. This made our deployment process easier since there was one less edge case to check.
Let me know if you have any questions!