Suppose I have Drupal and CiviCRM installations to automate.
These, however, need particular configs for working together (some file edits and database configs)
Should I make a fixed version install (eg. Drupal 4.7.5 + CiviCRM 4.5.6), install them and configure, and then save the edited files plus database?
Or should I put more effort in my build script and make some queries and seds to edit those configs in the database and files?
Your question sounds like you should have a look at what I call Features Configuration Management, aka FCM. FCM is not only about using Drupal's Features module, and not about Configuration Management (as introduced in Drupal version 8). Instead, it is a special case of Software Configuration Management, aka SCM, applied to Drupal.
Mostly because Features can be considered as a code generator, whereas that generated code may be considered as the build script (as in your question). Which can then also be used to be migrated through multiple environments.
Have a look at my (popular) answer to "How to use the Features module in a 3 dev environments?" for (way) more details about all this.
