The reason for this difference is that the timing score reported in SmartXplorer is coming from the timing report (*.twr), not from the PAR result.
The unconstrained timing report may include hold errors that are not explicitly covered by user timing constraints.
For more information on this issue, pleas see (Xilinx Answer 37292)
If you set the -u switch for trace, and there is a timing error in unconstrained paths, SmartXplorer will report a different timing score than the PAR result.
This issue also occurs when the -a switch is used in the trace options (-to) for the SmartXplorer command.
If you remove the -a switch then the correct timing score is reported in the SmartXplorer Summary.