If you could wire the I2C pins to a connector, and add a USB-Serial device (CY7C65215) between your processor and the I2C connector, then you could directly test the EZ-PD Configuration Utility. You could also use the USB-Serial device on the CY4531 EVK and connect the I2C pins from J6 header on the daughter card to the CCG3 on your board.
No, the EZ-PD Configuration Utility is meant for I2C programming while the SWD programming is done through PSoC Programmer using MiniProg3/4. Please refer to the KBA for more details- CCGx Programming Methods - KBA97271
I would recommend buying the latest MiniProg4 programmer, although both of them are compatible with CCG3.