My friend Jaliya Udagedara has written nice post here, explaining how to deploy a Core web application into Azure App Service Application virtual directory. Below is comparison of few more settings you can use with Azure virtual directories.
Virtual directory settings with or without wwwroot works – without wwwroot
Publish settings – Site Name and Site URL
Deploy as site/en-ca with above settings
Deploy as site/wwwroot/en-ca
Both settings Works fine