Because being a supervisor of something isn't comparable to being the literal creator, writer and artist of something, at the end of the day Kubo isn't the director or producer of the anime, he's literally not even listed as one of the core staff for it on the
TYBW Anime website.
Kubo has entire control over the manga, the same cannot be said for the anime at all as there's like four or five different people who each have more control over it than he does, he's pretty much just an advisor who's input and ideas strongly influence the anime's direction, but he doesn't have the control to just do whatever he wants and supersede the director and writer, I mean, he literally states in the interview that he sends ideas to the anime staff and
hopes they make good use of it, that's completely indicative of the fact that he's not running the show.