Why did the Yu-Gi-Oh! anime change the dueling boxes/tables used in Duelist Kingdom to large platforms?

The biggest most likely reason is that the Yu-Gi-Oh series was actually heavily based on the manga back in 1998-1999. The show lasted 27 episodes. However in 2000, Nihon Ad Systems and Studio Gallop did a second adaptation taking the anime down a different path, tying it in with the trading card game. Since they were tying it in with the card game and that the target market was children they probably thought that it was a fun and inventive way to experience the duels in the show similar to how you would experience a real duel in real life.

Sitting down in an enclosed box that displays holograms of a small size doesn't spruce up the intense battle scenes that the manga wants to convey to the audience. Also sketching huge monsters as holograms in manga comics is difficult keeping in mind that the dueling field needs to showcase both the monsters and the duelists. It would take up a large space on the page.

Also when the anime was being created, the emphasis was made to make duels more interactive than just showing monsters screaming. Like monsters could now be launched from canons, Gaia the Fierce Knight could now gallop and much more.