Yes, the data is not perfect.
I don’t know the complete story, but it looks like the json file was made by someone here. There are nearly two hundred countries and they do change. Presumably someone originally wrote it out by hand, maybe copied the data from somewhere. The file is over 500 lines long, so I don’t think anyone is in a big hurry to jump in there every time some country changes flags or borders. But you can edit the existing one and make your own. You might even find who is maintaining that repo and send it to them.
The flags are a little harder because that appears to be a separate company. If you have concerns, you can always contact them. Or you can edit the sprite yourself and make changes.
I wouldn’t worry about it too much. It’s not meant as a political statement - it’s just a set of data to work on. I know people get touchy about this stuff, but it’s just hard to maintain a free service run by volunteers. Maybe when you’re ready you can volunteer yourself.
But if you can find better data source, you can use that. In theory you could use other data (US states and Canadian provinces, relationships of Game of Thrones characters, etc.) - I don’t think anyone would mind if you used different data, as long as you are demonstrating the same coding skills. You just need some data set that will allow you to build a non-trivial force-directed graph.