From the ST3 API docs, it seems that most of the paths are relative, either to Packages
or Installed Packages
, depending on the class/method you're looking at. Since plugins should be designed for portability between 3 different platforms, and between standard and portable installs, relative paths are a good idea. Try setting your code to:
MyOutputView.set_syntax_file("Packages/MyLang/my.tmLanguage")
MyOutputView.settings().set("color_scheme", "Packages/MyColorScheme/my.tmTheme")
and you should be all set.