Issues using upgrademodx extra

I'm pretty sure that's a problem with Setup (UGM is no longer running at that point). Setup asks you where the core directory is in order to find the the main config file, but since you've changed the config key, it's not called config.inc.php. When it doesn't find that file, Setup assumes it's a new install.

I think you could fix it by editing the config.core.php file in the setup/ directory and correcting the config key.

Setup should really be looking at the config.core.php file in the MODX root directory, which would give it both the core path and the config key. Then it wouldn't have to ask you anything if the core is moved.