I wouldn't say there's "absolutely nothing wrong with it". Someone may have a valid use case to leave a database server exposed to the public internet, but they probably don't.
The only things that should be public facing are things that clients need to access directly. In most cases, that's just an HTTP server. In GitLab's case, it's an HTTP server and a git server.
One of the most important principles of infrastructure security is to minimize the attack surface. No matter how locked down you have it, there are always zero days and other exploits out there. This is a concern even if you block the database port at the firewall but leave some other services (like SSH) open; if any of those services get compromised, it has the potential to allow for the compromise of the rest of the box.
If there's no need for the public to connect to the server, there's no need to take the risk of leaving any of its services open. And if there's no need to have its services open, there's no need for the box to even be addressable from the public internet (i.e., no reason to have a public IP address).
Put the server on the internal network and connect over a secure mechanism like VPN and not only do you not have to worry about strangers connecting to your servers, you don't have to worry about whitelisting or blacklisting individual IPs in your firewall (instead, you whitelist the applicable internal subnets, which should also be restricted based on resource access level), you don't have to worry about your firewall's rules getting wiped for whatever reason and accidentally letting the whole planet in (common if you use iptables, most distros manually require the admin to configure iptables-restore to run on boot), don't have to worry about someone zero-daying your SSH or FTP daemon, don't have to worry about the box being affected by network-level attacks like DDoS, which can sometimes target whole subnets, and so forth. Just much tidier and safer all around.