I found the culprit… It was there, in front of me, the whole time.
It seems that Xamarin Studio adds the following line to the csproj:
<AndroidApplication>True</AndroidApplication>
This overrides the output type for Xamarin MSBuild tasks. Setting it to false or simply removing it makes everything compile and work just fine.
I have checked the vanilla csproj generated by Protobuild and this line is not present. This line appears in the csproj file if one tries to edit the project properties or import the csproj into another project. I think that Xamarin.Android consider that it is an “Application” because of the presence of a manifest.xml file and will add this line if it has to update the csproj file.
So, it’s definetly not a MonoGame or Protobuild issue, but a Xamarin.Android one which wrongly adds metadata to the csproj if the project is imported or modified. I will report back to Xamarin and hopefully this will be patched.