When your design has been programmed into the Xilinx device, the recommended GT transceiver power-on sequence to achieve minimum current draw is specified in the Data Sheet: DC and Switching Characteristics for the applicable device. The recommended power-off sequence is the reverse of the power-on sequence to achieve minimum current draw.
If the recommended sequences are not followed, current drawn can be higher than specifications during power-up and power-down. XPE calculates GT power assuming the recommended power-up, power-down sequence is used by the design, and the power numbers reflect this.
To calculate the extra power as a result of not following the recommended power up/down sequence, consult the Xilinx Answer Records.