Per this discussion between reduz and Zylann:
It should be possible to debug tool scripts running in the editor.
This provides an example of debugging a scene running outside the editor with the -d flag:
However, it doesn't stop to allow the addition of breakpoints before the scene starts executing.
We can start the editor editing the scene like this:
godot -d -e my.tscn
However, that also loads the editor immediately without stopping to allow breakpoint entry and does not recognize any breakpoints set on scripts in the editor visually, which are lost when the editor closes.