Is it an unsafe practice to symlink /etc conf files?

I noticed you add git as a tag--it sounds like /home/ubuntu/etc-config is a git repository with all your configs in it. In which case, it sounds like you're trying to manage configuration files from a central location. If that's the case, I highly recommend looking for a real solution.

Take a look at something like puppet, chef, cfengine, or any of the major configuration manage engines out there. Many of them are free and open source, widely used, and are typically very easy to setup and manage. If you're trying to use a "lightweight" method instead, you'll likely come to regret it later.

If these are on different filesystems, then this is a very bad idea. If the other filesystem does not mount then you will have problems.