Bleh thought about adding my point of view, so might as well
I'd say that the manga adaptations must have had connections with the actual owners of Pokemon - the fact is that they were released by companies like Viz Media and Chaung Yi which sell/distribute such materials over the world (Authors gave it to them to distribute and stuff)
This means that a profit is being made (Well not necessarily a profit, just any money) which is a direct breach of copyright law, if prior consent is not obtained from the creators of the Pokemon Franchise.
Think about it. How would one of the authors be able to distribute his work around the world? Sure the internet, but the manga adaptations that are 'recognised' are distributed in paper volumes, so it's impossible for them to have done it profit-free. They would have had to spend money distributing it, and no they probably did not spend thousands of dollars from their own bank accounts to show off one of their mangas.
So basically. These mangas will have had some connection to the actual owners since they're a profit-based endeavors and required prior consent. However adaptations created on a non-commerical scale for no profit whatsoever can be done without prior consent.