Thanks for the follow-up and updating the question. Apologies for any issues that you may have encountered while submitting the question.
If my understanding of your scenario description is correct, you are having an issue with the Yoast plugin and the default .azurewebsites.net domain being saved in its database tables. Typically, you will update and configure the plugin in a similar way as you would host a WordPress site on-prem.
Based on your requirement, you may consider to manually update the URLs in the Yoast plugin to your custom domain URLs. This could possibly prevent the default .azurewebsites.net domain from being added to the page markup as the canonical URL.
If you are looking to disable the default WebApp URL assigned to the Azure WebApp.
You may add a 301 redirect rule on WordPress.
Create Nginx redirect rule, as outlined in this discussion thread.
Ref: Map an existing custom DNS name to Azure App Service
Kindly let us know with more info about the issue.