Yes, they do. The figures online are often out on the shelves in the store (which is why sometimes you can try to buy something and they'll say, "sorry it's sold out!"
The Mandarakes are all kind of disorganized. There are sections for figures, and all the figures will be there in one area more or less, but there's generally not a lot of rhyme or reason to how they're laid out, especially at the two in Osaka. The one in Akihabara seems to be the most organized, and the one in Shibuya is somewhere in the middle. Some of them specialize in particular material. Also, god help you if you go to the Mandarake in Nakano Broadway. It's spread out into different shops all over a 3-story mall. Ask an employee for an English map.
