On the number of versions, try changing line 416 of the core\components\upgrademodx\model\upgrademodx.class.php file
from this:
$retVal = $this->finalizeVersionArray($retVal);
to this:
$retVal = $this->finalizeVersionArray($retVal, $plOnly, $versionsToShow);
On the config key -- UGM uses the config key defined in config.core.php to find config.inc.php. Apparently the traditional distribution doesn't (and doesn't gracefully recognize the moved core either). I don't download the advanced version because it won't run on some servers and requires a different process to put the files in place.
I've argued for a long time that the traditional and advanced distros should be unified or at least that the traditional one should handle a moved core and renamed stuff without user intervention.
As a workaround, I think that you could temporarily create a copy of your config file with the traditional name. After the upgrades, you could check to make sure it hasn't changed. If it has, you could copy it back to your custom file.