To create a shortcut with a relative path, set the target to the following.
%windir%\\system32\\cmd.exe /c start your_relpath\\app.exe [your_args]
For a portable shortcut, that works with a relative path, use the following:
Simply drop this in the "Target" of the Shortcut Properties:
%COMSPEC% /C "start GoogleChromePortable.exe -enableextensions -incognito"
Expected behavior: A brief CMD window will popup and close just prior to chrome launching.
Note: the "Start in:" option can be left blank. Also note, the .exe is located in the same folder as the shortcut, but move the folder and the shortcut works just fine.
This is confirmed to work in Win10 1607.
Credit: some other post on stackoverflow a while ago.