The CyClocksRT uses a proprietary algorithm to optimize the charge pump value. The table 9 in the datasheet will give you guaranteed PLL stability, but will not necessarily be the optimum solution. It is recommended to refer 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.
CyClocksRT goes from the highest charge pump setting and calculates the loop bandwidth, if the phase detector frequency, which is equal to VCO/P, is 5 times greater than the calculated bandwidth it will stop searching. Otherwise it will go to the next lower charge pump setting and go through the calculation again.
This is why you see values from software different from the table 9 in the datasheet.
The charge pump values that you get from the table 9 in the datasheet are valid entries, and will give you a stable clock output.
The values generated out of both CyClocksRT and table 9 will guarantee stability. There is a range in which the charge pump can be set and the values from table 9 are usually around the center of that stability region. CyClocksRT will try to get to the optimum area of the stability region.
So it is strongly recommended to use CyClocksRT for jedec file configuration that should be used for programming the device.