That is indeed a good question and I don't have the answer. As nobody answered this thread when I created it, it's probably better for you to create a new thread.
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I got a response from Cypress that it should be VDDIO0. I did some tests and it seems I can program the eFuse regardless of the voltage. I tried on the BLE Pioneer board at 1.8V and 3.3V and my own board at 1.8V and all were able to program. Has anyone seen eFuse programming fail because of bad voltage and at what voltage?
The EFUSE bits are guaranteed to be programmed only when the voltage on the VDDIO0 pin is 2.5 volts. At other voltages the EFUSE bits may be programmed but not guaranteed by Cypress.