"tools" in the context of Godot compilation means "Godot Editor". The tools=yes option therefore means that you want the Editor to be included with your executable.
For a list of options supported by your executable, run it with -h.
If you want to use your executable as an interpreter to run tool scripts (tool scripts being scripts that can be run in the Editor, denoted by the tool keyword), you can write --script my_script.gd. See OS.get_cmdline_args().