I would have thought that Setup would find the core based on the config.core.php file rather than having to ask you. Did you maybe overwrite the config.core.php files when you copied the files?
The setup checks the existence of "core" folder by name, if it is not one level up from the script file then it will ask you about it's location before proceeding further with setup.Even if you modify config.core.php with core location, setup will perform what i just mentioned. I do not remember exactly which files i modified but i have ran through all the config files (manager, core, root, connectors etc. ) to be sure that every thing is correct.
index.php will access config.core.php to get core path, then from there it loads modx.class.php
manager and connectors have their own config.core.php and go through similar cycle to get into modx.class. important for each part is to be able to define MODX_CORE_PATH where they expect where to find things inside it, i have manipulated with that part as well and changed folders and includes structure for extra hardening
(for security researching purposes) i could do that and everything was functioning properly, where my pentesting team got stuck and had no clue where is what, but upgrading such environment was hell, but it was a pentesting environment not production anyway. Sorry for the long story but thought it might be interesting.
With regards to the difference between advanced and traditional, i assume you already know about this link:
http://rtfm.modx.com/revolution/2.x/getting-started/installation/advanced-installation
in short, the advanced package makes it easier and gives "more" options for hardening, but from my testing, i personally prefer the traditional, where everything is in place, and i just have control which files to merge where, in addition, my experience with advanced package wasn't pleasant while performing extra hardening as upgrading ALWAYS failed for me
(yes everything can be troubleshooted but for me waste of time if traditional was easier). Thus i decided to be stuck with traditional package. Depending on each person's preference of course, advanced should be easier for basic hardening.