The comment with respect to PDA and aircraft operating at a higher than planned weight is not valid. PDA is only to address fuel burn increase due to engine/airframe deterioration.
One of the issues with APM type software is that only the cruise phase of flight is considered and corrections for weight changes are sometimes problematic. The ideal way to derive PDA values is to use APM values and also do comparative BURN studies (plan vs. actual) for each specific aircraft where the data is normalized for weight and time changes. This produces a PDA value for all phases of flight. The weight/time data normalization exercise is the key to getting the PDA value correct.
Technically LRC and CI 0 are not mathematically connected. LRC is 1% less than MRC. CI 0 and MRC are close but not the same.