How should I use 3.3V + 5V in KiCad without getting an ERC error?
Those pins are defined as bidirectional in the part library, which means that they could sink current (by trying to set the pin to 0).  So the ERC is -- quite correctly -- flagging it as a potential problem.

If you're absolutely positively never going to use those pins as I/O, then copy that part into a new library part and define the pins as inputs.  It's probably safer, if you have the room, to pull those pins up through resistors (10k\$\Omega\$ is a nice round number).  That way if someone messes up the software and sets the pins to I/O they'll just harmlessly pull their outputs low, at the cost of some supply current.