There's currently no way to add new games to a template file (i.e. create your own template). There's a "UnknownID" line in there, which no one can figure out where/how they generate it. That line was meant to stop Chinese cloners, not a to thwart Nintendo. But they failed anyway. There are sky3ds clones out there. Yup. And they just use the sky3ds template file. So good job on that, "
sly 3ds" team... (sarcasm)
People can use custom headers from legit cartridges to "merge" them with existing template files in order for their ROMS to appear legit online. But that's about it. And you may as well play the games as CIA instead, since they don't use headers.
To add a new game to the template file you need to send some kind of information to the sky3ds team to add that game for you, if it's not already in the template file. And that can take days or even weeks. Read this thread:
https://gbatemp.net/threads/what-to-do-with-roms-that-arent-supported-yet.390440/