When you use an expression template and you also want a theme, you should use a template theme.

The following configuration should work:

{
   "Name":"Console",
   "Args":{
      "formatter":{
         "type":"Serilog.Templates.ExpressionTemplate, Serilog.Expressions",
         "template":"{@t:HH:mm:ss.fff zzz} | {@l:u3} | {@m}\n{@x}",
         "theme":"Serilog.Templates.Themes.TemplateTheme::Code, Serilog.Expressions"
      }
   }
}