If False septon is in play can I use Braavosi Harbormaster to lower gold penalty?

Yes.

Specifically lowering the gold penalty is not the same as reducing the cost. (For example, if the gold penalty on a card is only 1 - say because of the True Queen Agenda - the reduction of 2 from the Harbormaster does not feed into lowering the rest of the cost. So lowering a gold penalty and reducing the cost are not really the same thing.)

Thank you, this question was confusing me.

Well, the confusing part comes from the fact that the gold penalty is a component of the cost. So something that lowers total cost can effectively off-set a gold penalty by lowering total cost after the gold penalty is added in. But Harbormaster lowers the gold penalty before it is added into total cost. The relationship is "one-way" so it can be counterintuitive.