It's simple. If you look at the schematics for the cy8ckit-059 you will notice a schottky diode D1 on the KitProg board.
VBUS is connected directly to the 5V source from the USB cable from the host computer. VTARG is the voltage directly connected to the PSoC5LP target CPU. The Schottky diode drop is about 0.1V to 0.3V (depends on the load current. Higher load currents have a higher drop voltage.) Therefore in your case, the diode drop is about 0.15V to provide you with 4.85V. The info I spotted on the internet that the source voltage variation can be from 4.75V to 5.5V. This is without the D1 voltage drop.
May I ask why a 5V accuracy is needed?
If this is because you are using the 5V supplied to VDDA for use with the ADC vref, I recommend using the internal bandgap vref instead. This bandgap vref is virtually immune from VDDA (or VDDD) voltage variances. It is significantly more stable.