V_CL are already above the voltage where the internal protection diodes of the microcontroller would activate.
There is nothing wrong in activating internal protection diodes.
What can be wrong is to allowing the current going through these diodes to be higher than value that can lead to latch-up.
I think typical value for this current limit is 20mA (probably can be found in datasheet).
If V_CL is for example 7.7V then (7.7-5.7)/20m = 100Ω between ESD protection and IC pin will limit internal diode current to safe value.
I am not using any protection at PDI interface (ATXmega 2 wire In System programming). I put at PCB 3 holes from 2x2 1.27mm pin-header near the IC. It takes not a lot of area. I shifted holes a little to make pin header (with one pin removed) used to connect during programming not be too loose in these holes.
In production interface is used only once for few seconds and then it is not exposed to ESD. We never noticed any problems with this.
You can see it in use at PCB here:
https://forum.kicad.info/t/approaching-pcb-track-routing-for-a-newbie/36302/8