Root directory at SFTP SSH is not the root directory of my server

I'm running into an issue with my server setup. The ssh credentials I use to SSH into my server don't put me in my root directory. Instead, if I ssh into my server, the directoy I'm in is /home/master. However, within the SFTP configuration, the root has to be put as /, since . or ~ are not excepted. Equally, due to the SFTP process within PHPStorm, it doesn't look upstream from the SSH home directory, so I can't specify that the root path is actually /home/master. This will through an error from SFTP that it can't find the specified folder in the path. However, if I were to use this path, and then open it in an SSH terminal, the path functions as expected.

This means that when rsync tries to fetch files, say from /applications/my-application/public_html, it will attempt to change into the directory /applications/my-application/public_html. However, the actual file path would be /home/master/applications/my-application/public_html. Due to this, I can't pull a specific folder down from the server for local use. Instead I would have to download the entire directory, with rsync changing into the absolute root (/) directory, which includes other configuration files for the server itself.

Is there a way around this so that I can pull down a specific file? Or is this a bug?