When check_all=True was passed,
- `os.path.join(bpy.utils.resource_path('USER'), "scripts")`
was used instead of BLENDER_USER_SCRIPTS.
- `os.path.join(bpy.utils.resource_path('SYSTEM'), "scripts")`
was used instead of BLENDER_SYSTEM_SCRIPTS.
Other minor changes:
- Simplify collecting paths.
- Don't add user-directories multiple times when check_all=True.
- Normalize paths before before checking duplicates to reduce the
change the same path is added multiple times.
Found these issues while investigating T101389.