Setup exe file version when publishing with dotnet

No, the main build output of your project still is a .dll file, the .exe (or linux, mac executables) file is a copied and renamed dotnet.exe (or in case of upcoming 2.0 versions, apphost.exe with the dll name to run embedded).

The exe file is only a helper that boots the runtime and then loads your dll. However, you can try to use binary editing tools like editbin.exe (VS C++ Tools) to modify the file after publishing.