Standardize drupal_set_message in system.install

A discussion stemmed off of this issue that brought attention that there isn't a standard way of displaying a message during a system update.

Some instances use:
drupal_set_message(t('My message'));

... While others use:

$ret[] = array('success' => TRUE, 'query' => $message);

This should be standardized into one format and documentation should be written for which method is preferred.