CY8C4024LQI-S411(PSoC4S) device can work watchdog without WCO. If you do not want to mount WCO, you can ignore C9/C12 capacitors.
Also, C3 capacitor does not used for CapSense operation or watchdog.
The WCO in the PSoC4000s has the only one function: to trim IMO, higher the accuracy from 2% to 0.2%.
The inner clock ILO is the source clock of WDT.
So it is Ok to use P0.4 and P0.5 as the capsense pins.
In addition, you don't need to populate the bypass capacitor on this kit as this is intended for future use.