What does the third tier of this skill mean? What effect does it have on carriers?
As stated above, it lets you get zero flux boost for up to 1% of your ships max flux. Unfortunately, this means that you only get it for having your shields up or firing really flux cheap weapons whose flux/shot doesn't take you above 1%. Some ships though have such poor flux stats or high shield upkeep that they lose the bonus when they raise shields because 1% is so unforgiving.
Carriers are locked into at least 5% of their max flux when set to "engage" to prevent them from benefiting from this and essentially having a permanent +50 speed boost.