Model-view-controller (MVC) architecture is optional in Drupal. MVC is accomplished by generating data in modules then theming the data in your theme.

Some modules format the data before output, which is not MVC.

Some modules format the output and provide documentation in how to reformat the data in your theme, which is MVO, Model-view-optional.
The best modules structure the output data using only classes and ids. They provide documentation on how to apply formatting using theme functions and CSS in your theme. They pass all output through t() to translate text and theme() to apply themeing. They supply a default CSS file so your data looks ok until you get around to developing your own theme. They are pure MVC.

When you use Drupal and find the odd bit of data that is not easily themed, there is an easy way to request a change to the relevant module. The module can be updated to theme the data in the standard way.