The last line of the generated project files (ProjectName.csproj):
<Import Project="$(MSBuildExtensionsPath)\Microsoft\XNA Game Studio\Microsoft.Xna.GameStudio.targets" />
Causes all references become missing and outputs the warning message "The referenced component 'System' can not be found".
It seems that the behavior of "$(MSBuildExtensionsPath)" referenced in Microsoft.Xna.GameStudio.targets has changed from "C:\Program Files (x86)\MSBuild\" to "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\MSBuild\"
By copying the "XNA Game Studio" directory from the old to the new directory, the problem is resolved.
I'm using Windows 8.1 if it matters.
Thank you so much for the work on the plugin. Now I can finally save some space by deleting old Visual Studio versions.