Some companies have always been terrible about this. Fan projects involving companies like Nintendo or Take Two Interactive (GTA) are like lawyer bait. Disney has hired lawyers to sue a daycare center that had (clearly unofficial) character art painted on the walls. It's dystopic, but it's the world we live in.
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".
Just gonna point out that the Nintendo going after fanworks bit is a tad blown out of proportion, especially online. They're definitely known for being way too heavy handed (especially compared to the likes of Sega), but they're not exactly going after every fan project they see on the internet. Large sites whose entire purpose is to host fan games and mods for the Mario, Zelda, Pokemon, etc series have been up for decades without any issues, and most mods and homebrew projects for consoles older than the Wii U or Switch are going fine.
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.
It's just so surprisingly tone deaf when things like this are done by companies that exist purely within the goodwill of their customers. Nothing that funko brings to the table has inherent value. If they have any world outlook other than to love their customers as much as they can, then they will fail in a time measured in quarters.