In free, open-source software, where the work is done by a diverse crew of overworked volunteers, the instructions don’t always keep up with the code.
Your discovery is exactly what the "bugs and requests" link is for at the top of the page. People often find their own solutions in situations like this but fail to report them so they can hide for months. Thanks for reporting on your experiences.
Reporting them on Jira Tracker (the "Bugs and Requests" link) greatly multiplies the odds that they’ll be corrected in a later release.
The most up-to-date install instructions are usually found here:
http://wiki.modxcms.com/index.php/Installation_Guide
. Unfortunatly, the Wiki is down at the moment. I don’t know when it will be back up.