I don't think that video's actually completely accurate. Well, I'm sure it's not accurate. We need to remember it appears to be a Korean video, and let's just say the countries around there are not completely honest with each other. The flag was adopted in the meiji-era, but I'm pretty damn sure that the symbol was used in that form before, during the Edo period absolutely for sure. Only some 300~ years before, but still.
IMO it's a political thing. Japan can't afford to let go of some things because it could be swallowed by outside forces. Not yet at least. There's so much pressure from outside to change, for the better or worse, that changing one thing will lead to another. One thing that comes to mind is in the Index series where the anime was forced to remove a character's rising sun design so that they can air it safely in China. Now it's very possible they will bend and remove other things as well, to keep in the market. If it's good or bad, you can decide. I don't like when an artist's vision needs to be tampered with to be "safe to show" just because of some symbol.
Anyway, I'm sure we all understand. It's not like the Japanese are hard-right militarists and have some kind of program to promote extreme-right radicalization. Maybe?!
But if it doesn't belong on the track, it's very weird why it was there in the first place. Maybe the track maker for the original track was ignorant and just decided to slap it on "because it looks cool"?
Somehow I doubt it's because of politics.