I didn't really expect Funko or 10:10 Games to be like that, but then again I didn't expect anyone would like Funko enough to make a fan page about their dolls.
Other companies allow fans to do pretty much whatever you want with their IP as long as you don't turn it into (too much of) a business. Sega has even hired a fan for their remasters rather than DMCA his project into oblivion.
When companies do this, I interpret this as the company giving a clear message: "don't be a fan of our work or we may apply legal pressure".
Unless a project is going viral in the media, raking up in a significant amount of money via a paywall or is directly competing with a current game, the chances of it getting shut down are incredibly low.
The courts have told Nintendo numerous times that they are in the wrong in this behavior and outlook. They have no legal means to keep Dolphin off Steam and it is a matter of judicial record that emulators are not an infringement of your IP on their own. Nintendo doesn't care and openly discusses their intent to make you suffer through lawfare. A just system would smack them down with a vexatious litigant label, but our system gives businesses infinite benefit of the doubt.