How to create a drush command without drupal?
1) Drush only searches certain folders for Drush commandfiles.  Run with --include=/path/to/your/drushcommands, or set $options['include'][] = '/path/to/your/drushcommands'; in your drushrc.php if you'd like to use a directory other than $HOME/.drush.

2) If you have in fact set your bootstrap to DRUSH_BOOTSTRAP_DRUSH, then you should not be getting that message.  Maybe there is something wrong with your commandfile definition; can't guess what it might be from the information provided, though.

For a quick start on writing a new Drush command, see the drushify project.  It will create a template for you very quickly.  Perhaps you could compare the template drushify creates with the commandfile you put together.