I had something like that in my previous samurai. Same size, not sure if it was a factory thing or not. It wobbled around, and I thought it kind of interfered with the e-brake a little bit. Personally, I liked having it for the armrest, but I ended up storing a bunch of junk in it so I got rid of it. Then I liked having the space back. It kind of opened things up.
Come to think of it, it was kind of handy for storing beer!
-Adam