Selecting a different flex option allows you to choose whether your board will have a softer or stiffer flex as opposed to the board's usual flex pattern. The boardmakers will optimize the construction for you so you get what's best for the board you choose.
A softer flex can provide a more free, more surfy ride, and can be appealing to riders looking for a cruisier sensation. Lighter riders around 140lbs and under might also appreciate a board that's better tailored to their weight.
A stiffer flex can increase freestyle capability and a board's high speed stability. If you're over 250 lbs, this can be a useful customization feature.
A custom board can take a month to produce and ship.