Onboard to current version of PNP powershell

[v-nom]

Hi. I am trying onboard to the latest version of PNP powershell in one of our Azure Automation accounts. I have been using this document as a base : https://pnp.github.io/powershell/articles/authentication.html#setting-up-access-to-your-own-azure-ad-app

But I have not been able to complete the instructions because the Register-PnPAzureADApp command asks you to sign into Azure. The tennant we are using requires you sign into AAD with a certificate and the pop up for that does not appear when running this in powershell. I have tried to replicate Register-PnPAzureADApp by creating my own app registration and uploading a certificate to it. But now I am unsure how to make the rest of it work. What permissions should I be requesting?