In fact, it wasn't just his digestive system. Dyon replaced all the smooth muscles in his body with ones he could actively control. For a mortal, this would be a nightmare. However, for Dyon who had such strong soul strength, it increased the efficiency of his body to godly levels.
Now, he could at will control how fast his heart beat and how fast he digested food. Like this, he could not only use them to greater extents when he needed them, but when he didn't need them, he could completely turn them off, saving his energy from being wasted.
The last thing Dyon did to his organs was apply the very same defensive abilities he gave to his bones, allowing them to disperse attacks with greater ease without becoming injured. Finally, he shifted the place of his organs from their original locations as a minor life saving measure.