Kitprog is using SIO Pins to do the programming communication.
This pins have a reference voltage input which is used to adjust the levels.
Saying that the other I/Os you mentioned are not adjusted and run with 5V.
If you want to run the PSoC with 3.3V you will need to snap of the KitProg and connect the programming interface of it seperatly.
I have prepared some time ago a video addressing the use of KitProg with 3.3V Targets:
In case you are running the PSoC with 3.3V the I/O pins are not 5V tolerant.
All the Best
Great information, I will include level shifters for the UART and I2C.
Thank you for taking the time to make that video!
SIO supports programmable output level and programmable input threshold. The logic is to sense the voltage level using ADC and adjust the SIO pin output. We have also implemented similar functionality for UART and I2C pins internally. Thus there is no need of level shifter at these lines. Please let us know if you face any discrepancies. We tried to recreate the same and observed 3.3 V at SDA lines without level shifter.