Agreed - replacing a hardware device with a digital pot which contains a bunch of registers, non-volatile or not, increases the state complexity of the system. It may make a better system, but it makes a different system which needs to be tested differently.
The ESD /EMI compliance issue is just one manifestation of this.
Also: make sure you choose the right version of the pot chip, you don't want your systems to be powered up first time, set at the wrong end of the pot when you want it to be set in the middle.
Had a colleague try this in a design. Worked well until ESD testing. Just wanted to present that potential pitfall. Ended up re-purposing that digital pot control output to PWM into an RC filter. The RC filter output was connected to a resistor which went into the feedback node of the regulator. The micro was always reading the voltage out of the regulator. It was an obvious solution once realized that the feedback node is ideally a fixed voltage; lower value than specified = more power commanded out. Makes for an easily configurable and adjustable power supply.