CyClocksRT uses a proprietary algorithm to optimize the charge pump value. The table in the datasheet will give you guaranteed PLL stability, but will not necessarily be the optimum solution. We recommend referencing the CyClocksRT charge pump value for critical configurations.
The datasheet values are set to cover a wide range of possible P values, while CyClocksRT knows exactly which P value you will be using.
The datasheet table chooses the lowest charge pump value acceptable for a specific range of P values; the lowest value will give you the most stability margin.