Application Tax Options

We are in the process of moving from an upgraded 11i tax regime to a new tax regime and tax configuration that uses R12 Tax Rules rather than the old 11i defaulting hierarchy (and Direct Rate Determination rules with Tax Classification Codes). I've been following the steps as per the document Case Study:  How to Switch From an Upgraded Tax Regime to a New Tax Regime - Canada HST example (Doc ID 1062897.1)
However, this document doesn't mention disabling the Application Tax Options. I'm unsure whether I should Inactivate them, or leave as is. What are the impacts of leaving them as active?