When the config.php file is created through the install interface it adds the line automatically.
From that page:
If you are installing a brand new XenForo, rather than upgrading from an existing version, you may include emoji support from the outset. The installer will add the necessary line to your src/config.php file automatically, if you allow the installation system to build your config file for you.
I, and I'm sure others, would expect the file labelled as "default" to have similar contents to what you would get by having the install process build it for you. I think we're fine to leave it up to XF to determine whether this is intentional or not