Personally I believe that whoever is doing the copyright abuse either is the original developer of the game or has some sort of relationship with them. Even though the "international copyright registration" site has no real authority, the documents they submitted include high-res 3D renders of models from the game, design documents, and source code commented in Japanese, none of which were publicly available prior to the copyright "submission". I don't think it's just some random crazy person. It's true that they're behaving in a strange way and utilizing shady overseas institutions, but the owner of Rodik is listed in the Panama Papers as having an offshore company in the Cayman Islands ( https://offshoreleaks.icij.org/nodes/74594 ) so that fits his MO.

As for motivation, in Japan there's much less of a cultural norm around sharing information publicly compared to the West. It's much more "if I have this thing and you don't, and I don't know you, why should I give it to you?" Some people will even get annoyed with you if you follow them on Twitter and you don't know them, or if you link to their website without asking them first. With that context, I don't think there needs to be much of a motivation beyond "people are posting videos and copies of my game online and I don't want them to".

Of course whoever is doing this doesn't seem to want to make themselves known publicly besides all the takedown notices, so I doubt we'll ever conclusively find out who they are. Much of what was being taken down is valid fair use, so even if it is someone associated with the original developer I don't really feel sorry for them getting their automated takedown request powers taken away.

In fact they just spent a few thousand dollars according to the article. But they cost the museum probably 200k+ in time and legal fees - asymmetric copyright warfare.