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The advanced option only has setup and core directories. You move the core to where you want it, then run Setup and tell it where your core is, and what you want to name your assets, connectors and manager directories, and optionally what you want to name the config.inc.php file. The setup then uses the vehicles in the core directory to build and place the core files and the other directories in place.
The standard installation has the build already done and the files in place, and just sets the config.inc.php file information and populates the database.
So they are totally different packages.
I don't think a new user of MODX can make an informed decision on which distro to use. In fact, I'm not sure I can based on the information on the download page.
I'm sure it's on the roadmap somewhere.