Alternatives to editing civicrm.settings.php
I'm assuming you're talking about DEFINE statements since you mention domain id? Are you able to edit drupal's settings.php? If so you can just put those DEFINEs in there since it loads first and most of the DEFINE settings in civicrm.settings.php check for if (defined(SETTING_NAME)).

If you can't edit drupal's settings.php, I haven't tested this but can you write a little drupal module that sets those defines, and in the system table set that module's weight to something lower than the weight for civicrm so that it runs first.

If you're talking about various $civicrm_setting['xxxxx'] entries, then again I haven't tested but the module method might also work but you would set the weight higher than civicrm's weight, so that it loads after.