How are Honest and Polite to work under the houserule, exactly?
Honest grants a +1 bonus to Persuasion when trying to negotiate with someone or convince them to agree to something or do something, so long as you are trying to "sweet talk" them, not threaten or lie. It causes you to take a -1 penalty to Persuasion when trying to lie, and to Perception rolls to read peoples body language and read in to their under-tone.
Because "You are naturally straightforward and sincere. This quality helps you persuade people to your viewpoint, but you have difficulty telling lies and seeing deception in others".
Polite grants a +1 bonus to Persuasion when trying to negotiate with someone or convince them to agree to something or do something, so long as you are trying to "sweet talk" them, not threaten or lie. It causes you to take a -2 penalty to Persuasion when trying to get what you want from someone using threats, or when trying to cow someone.
Because "You are courteous and well spoken".
In-game, these traits operate mechanically the same as they otherwise would without the houseruled skill re-write is the intent.