Specified framework 'Microsoft.AspNetCore.App', version '3.1.0' was not found for a Linux Azure WebApp
I've run into the same situation, using the information you provided I've been able to fix the issue by setting the value manually in the Devops Pipelines Build .yml file. It seems like they are just missing the value from RunTime Stack drop down. If you manually update the build processes .yml file as seen here:
This will select the proper framework version. Hopefully this will fix your issue with the Azure Devops CI Pipeline deployment.