If the flash is on manual, the flash exposure control doesn't do anything. If the flash is set to 1/64 power, it will deliver 1/64 power. Set it to 1/2 power and it will deliver 1/2 power. The flash exposure control only works with TTL flash metering.

1/128 isn't the flash's minimum possible power; it's merely the minimum power you can select using the manual controls. It used to be that auto/manual flashes "bottomed out" at 1/16 when physical switches were used, even if TTL or "auto" mode could supply much less power. Even going to 1/128 vs 1/64 means an extra character on the display. At some point, interface practicality and circuit cost/complexity have to be considered.

If you are working with manual flash lighting and you need less than 1/64 power (or whatever the lowest setting is on the flash) gives you, then your only options (assuming the aperture you're using is what's needed for the shot) to lower your ISO setting to something less sensitive or to use neutral density gels (or something jury-rigged that has the same effect) to reduce the output of your flash.