This is accepted use of the database, and the reason you see that line in the file. Adding entries after that line allows you to quickly identify local additions. It is common for the /etc/services database to be incomplete, so you may be adding some registered ports. Some tools will accept ports by name if they are available from /etc/services, or an equivalent source.
The one risk you have is loosing the additions when patching the O/S as /etc/services may be updated. Make sure you have a copy of the local services that you can quickly append to the new file. Consider automating the addition of missing entries to the file.
If you assign ports for services like NFS and VNC, this is a good location to record those ports. VNC has defined port ranges NFS plays better with firewalls, if you configure it to use fixed ports.
When possible, I would recommend using the IANA registered service ports, even if they aren't listed in the supplied /etc/services file. This can prevent future issues if they get added to the file.