How do you turn off comments, by default, for a module defined content type?
These instructions will enable you to identify and set any variable you'd like in Drupal 7. Please feel free to ask for clarification.

I'd start by installing the Devel module so you can see the variable you need to set. This will allow you to inspect the array where this setting is defined. 

Visit a node of the content type you're working with. You'll see a tab called "Devel". Follow it and you'll be able to see the array which defines a node of this content type. There should be a value called "Comment", and I believe it needs to be set to "1" to disable comments.

As a sidenote, the Features Overrides module does this by setting 
$overrides["variable.comment_mycontenttype.value"] = '1';

But, since we're not using that module, we'll set it manually.

You should be able to define that variable inside your module code by using the variable_set() function. 

That code can live inside hook_update_N(), which is executed when update.php is run. Simply add the code for your update hook inside your custom module and run update.php on your site.