Code sample confusion
You are headed into right direction: almost all websites I work on, have one main module that contains general customizations and provides the base for additional custom modules.
I find that this is absolutely necessary if you want to keep the sanity in the long run, especially if the project can potentially grow.

Small fixes are often faster and easier to maintain this way, rather than just adding more modules and making the configuration more complex.

I created a boilerplate module that we use as "Main" module for almost every Drupal installation.
You can see it here.

Most of the generic implementations / integrations (views, rules, webform, drush, helper functions, etc.) are there already, and it's much easier to just remove what you don't need.

On a related note, the same can be said for new Drupal installations. After creating a lot of Drupal websites for real projects and testing, you will realize that there are certain sets of modules and settings you want to have as a starting point. This is solved the best through installation profiles.

Here is a default installation profile that we use in almost every website, as well as for testing.

Hope this helps.