I have personally worked with Japanese* licenses like Pokemon and with Toho on Godzilla for consumer products and indeed "approvals" can be a nightmare. I can believe Universal's hands were tied. If it is a struggle for Universal to create a 9/10 E-ticket attraction in partnership with Nintendo, does that make anyone question whether the Epic Universe expansion plot next to DK is used for more Nintendo or to expand Dark Universe even more?
For example, I'd rather have an indoor suspended Dracula coaster -- Space Mountain-esque but where you swoop out of the darkness over and down through a village -- all housed inside a dramatic Transylvania mountain range... to challenge the majestic backdrop/placemaking Disney is proposing for Villains Land. With an attraction like this, Universal Creative has full control.
*And to clarify, I've worked with Blair Partnership/Harry Potter, Disney, Universal, and dozens of other studios and global licensors over 25 years. The reason I mention Japanese is because in my experience, as demanding as many licensors can be, I found the Japanese licensors to have more definitive and un-explained (literally, they wouldn't provide an explanation) requirements and limitations. It was often a black box type situation, where you waited months to hear back and it was just "no." It often felt like they preferred the project just not happen, like they "didn't need the money." It may have been cultural, I don't know, but it made things difficult in an already difficult field.