The is the only practical way to play a randomized Pokémon Y ROM on a PC or Android device. Unlike a 3DS console, Citra allows for:

Go to File -> Load File and select your newly created file, or double-click Pokémon Y in your library if you used the LayeredFS method. Essential Technical Notes

Randomizing a 3DS game can cause unique glitches. Here are the most common problems and solutions.