Every option available at ff6wc.com has a corresponding flag (noted on this wiki in parenthesis) used by the randomizer to apply the selected settings when generating a game.
Combined with a seed, flags define how a game will be randomized. Modifying the seed or flags (except those under custom) will change the resulting generated game. Conversely, using an identical seed and flags will generate identical copies of the game useful for competitive or co-op events. The share page provides a convenient link to a predefined seed and flags.
Please note that flags may differ between randomizer versions. Identical flags and seeds may produce different games before and after an update.